diff --git a/dev/articles/benchmarks.html b/dev/articles/benchmarks.html index c5605163..3e2525fc 100644 --- a/dev/articles/benchmarks.html +++ b/dev/articles/benchmarks.html @@ -166,11 +166,11 @@

Compared with other packages#> # A tibble: 5 × 6 #> expression min median `itr/sec` mem_alloc `gc/sec` #> <bch:expr> <bch:tm> <bch:tm> <dbl> <bch:byt> <dbl> -#> 1 heatmap() 145.63ms 153.56ms 6.41 139.11MB 3.20 -#> 2 heatmap.2() 2.24s 2.24s 0.446 224.23MB 0.891 -#> 3 Heatmap() 4.36s 4.36s 0.230 792.59MB 2.98 -#> 4 pheatmap() 644.69ms 644.69ms 1.55 124.1MB 3.10 -#> 5 ggalign() 2.46s 2.46s 0.407 2.51GB 10.2 +#> 1 heatmap() 144.09ms 146.62ms 6.59 139.11MB 3.30 +#> 2 heatmap.2() 2.26s 2.26s 0.443 224.23MB 0.886 +#> 3 Heatmap() 4.36s 4.36s 0.229 792.59MB 2.98 +#> 4 pheatmap() 663.6ms 663.6ms 1.51 124.1MB 3.01 +#> 5 ggalign() 2.4s 2.4s 0.416 2.51GB 10.4

For heatmap with dendrogram

 bench::mark(
@@ -215,11 +215,11 @@ 
Compared with other packages#> # A tibble: 5 × 6
 #>   expression       min   median `itr/sec` mem_alloc `gc/sec`
 #>   <bch:expr>  <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
-#> 1 heatmap()      2.63s    2.63s     0.380  173.72MB    1.14 
-#> 2 heatmap.2()    3.14s    3.14s     0.318  223.41MB    0.954
-#> 3 Heatmap()      5.43s    5.43s     0.184    1.51GB    1.47 
-#> 4 pheatmap()     2.27s    2.27s     0.441  177.53MB    0.881
-#> 5 ggalign()      4.86s    4.86s     0.206    2.58GB    4.11
+#> 1 heatmap() 2.64s 2.64s 0.378 173.72MB 2.65 +#> 2 heatmap.2() 2.78s 2.78s 0.359 223.41MB 2.52 +#> 3 Heatmap() 5.9s 5.9s 0.169 1.51GB 2.37 +#> 4 pheatmap() 2.26s 2.26s 0.443 177.53MB 0.443 +#> 5 ggalign() 5.11s 5.11s 0.196 2.58GB 5.29 diff --git a/dev/index.html b/dev/index.html index d2d6bce7..0ed8d62f 100644 --- a/dev/index.html +++ b/dev/index.html @@ -124,10 +124,10 @@

Compare with other similar toolsmarsilea -ComplexHeatmap +aplot -ggtree+aplot +ComplexHeatmap @@ -159,10 +159,10 @@

Compare with other similar tools -Functional +Declarative+Functional -Declarative +Functional @@ -176,10 +176,10 @@

Compare with other similar tools -grid +ggplot2 (Advanced plot system built on grid system) -ggplot2 (Advanced plot system built on grid system) +grid @@ -193,10 +193,10 @@

Compare with other similar tools -Heatmap +Composable Visualization -tree Data +Heatmap @@ -227,10 +227,10 @@

Compare with other similar tools -Heatmap Only (discrete variables) +✅ -Cannot arrange multiple QuadLayouts +Heatmap Only (discrete variables) @@ -238,23 +238,6 @@

Compare with other similar toolsCircleLayout -Arc with angle >= 90 - - -❌ - - -❌ - - -✅ - - - - -CrossLayout - - ✅ @@ -289,7 +272,7 @@

Compare with other similar tools -One-to-Many +One-to-Many/Many-to-One ✅ @@ -306,7 +289,7 @@

Compare with other similar tools -Many-to-One +Many-to-Many ✅ @@ -323,7 +306,7 @@

Compare with other similar tools -Cross +Crosswise ✅ @@ -339,20 +322,20 @@

Compare with other similar tools - -Ease of Use + +Annotate observations -Easy for ggplot2 users +✅ -Easy for python user +❌ -Easy for for grid user +❌ -Easy for ggplot2 users +✅ @@ -366,10 +349,10 @@

Compare with other similar tools -❌ +✅ -Limited Geometric layers support in CircleLayout +❌ @@ -377,76 +360,75 @@

Compare with other similar tools -----+++++ + - - + + - - + - + - + - + - + - + @@ -454,10 +436,10 @@

Compare with other similar tools

- + @@ -470,22 +452,22 @@

Compare with other similar tools3D Heatmap

- + - + - +
Specification ggalign marsileaaplot ComplexHeatmapggtree+aplot
Data input Various, and can be easily extended fixedfixed Various, and can be easily extendedfixed
Plot Type Wide variety, provided by ggplot2 Many, but limited✅ Many, but limitedLimited Geometric layers support in CircleLayout -
Reorder observations ✅ ✅Heatmap Only (Cannot be used in Stack Layout) ✅Heatmap Only (Cannot be used in Stack Layout)
Group observations into different panels ✅ ✅Heatmap Only (Cannot be used in Stack Layout) ❌Heatmap Only (Cannot be used in Stack Layout)
Clustering algorithm Kmeans,Hierarchical Clustering and arbitary algorithm ❌Kmeans,Hierarchical Clustering, but can provide clustering group directly ❌Kmeans,Hierarchical Clustering, but can provide clustering group directly
Legends Creation Automatic ManualLimited automatic, requires manual add AutomaticLimited automatic, requires manual add
Legends Position Anywhere, can be controlled for a single plot ?Four sides, can only be placed on one side at a time AnywhereFour sides, can only be placed on one side at a time
Scientific Color Palettes Many LimitedLimited ManyLimited
Dendrogram hclust only -hclust only (Cannot be used in StackLayout) Tree from Both hclust or ape +hclust only (Cannot be used in StackLayout)
Tanglegram✅ ❌✅ ❌✅
Oncoplot ✅ ✅✅ ❌✅
UpSet plot ✅ ✅✅ ❌✅
diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml index e33fdb49..c303500c 100644 --- a/dev/pkgdown.yml +++ b/dev/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: articles/benchmarks: benchmarks.html articles/FAQ: FAQ.html -last_built: 2025-01-20T15:38Z +last_built: 2025-01-20T15:44Z urls: reference: https://yunuuuu.github.io/ggalign/reference article: https://yunuuuu.github.io/ggalign/articles diff --git a/dev/search.json b/dev/search.json index 856b3aa3..6b8c8918 100644 --- a/dev/search.json +++ b/dev/search.json @@ -1 +1 @@ -[{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement yunyunp96@163.com. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 ggalign authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/articles/FAQ.html","id":"can-i-change-the-default-data-for-all-geoms","dir":"Articles","previous_headings":"","what":"Can I change the default data for all geoms?","title":"FAQ","text":"function ggalign requires specific data formats operations. need transform filter data individual geoms, can use data argument within geom. However, multiple geoms want consistent transformation applied across , can utilize scheme_data() function allows transform default data additive geoms.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/articles/FAQ.html","id":"why-are-there-spaces-after-setting-all-plot-margin-to-zero","dir":"Articles","previous_headings":"","what":"Why are there spaces after setting all plot.margin to zero?","title":"FAQ","text":"default, ggalign doesn’t add spaces plots. notice spaces, likely due : Plot margins within individual plots. Scale expansion automatically added ggplot2. can resolve removing scale expansion adjusting margins theme:","code":"ggheatmap(small_mat) + anno_top() + align_dendro(aes(color = branch), k = 3L) + scale_y_continuous(expand = expansion()) & theme(plot.margin = margin()) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/articles/FAQ.html","id":"why-cant-i-add-two-dendrograms-with-different-reorder-settings","dir":"Articles","previous_headings":"","what":"Why can’t I add two dendrograms with different reorder settings?","title":"FAQ","text":"Note: always prevent users reordering layout direction twice. reorder_group = FALSE used, reordering heatmap occurs within group. long ordering within group remains consistent, two dendrograms can placed axis heatmap. Let’s assume panels represents group observation index represents ordered index observations. code provided, panels initialized ungrouped index unordered: add dendrogram reorder_group = FALSE; ’ll something like (Since reorder_group = FALSE, panels won’t changed): However, dendrogram reorder_group = TRUE added, reorder panels, underlying index changed: prevent reordering axis twice, ensure new_index matches index (index NULL). done maintain consistency prevent conflicts ordering heatmap.","code":"panels <- NULL index <- NULL set.seed(2L) group <- sample(letters[1:3], ncol(small_mat), replace = TRUE) h <- ggheatmap(small_mat) + anno_top() + align_group(group) h1 <- h + align_dendro(reorder_group = FALSE, merge_dendrogram = TRUE) # always remember dendrogram will initialize the index, here, we extract the # index from the underlying dendrogram index <- stats::order.dendrogram(ggalign_stat(h1, \"top\", 2L)) h2 <- h + align_dendro(reorder_group = TRUE, merge_dendrogram = TRUE) new_index <- stats::order.dendrogram(ggalign_stat(h2, \"top\", 2L)) all(index == new_index) #> [1] FALSE"},{"path":"https://yunuuuu.github.io/ggalign/dev/articles/FAQ.html","id":"session-information","dir":"Articles","previous_headings":"","what":"Session information","title":"FAQ","text":"","code":"sessionInfo() #> R version 4.4.2 (2024-10-31) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 24.04.1 LTS #> #> Matrix products: default #> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0 #> #> locale: #> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 #> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 #> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C #> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C #> #> time zone: UTC #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] ggalign_0.0.5.9000 ggplot2_3.5.1 #> #> loaded via a namespace (and not attached): #> [1] vctrs_0.6.5 cli_3.6.3 knitr_1.49 rlang_1.1.5 #> [5] xfun_0.50 generics_0.1.3 textshaping_0.4.1 jsonlite_1.8.9 #> [9] labeling_0.4.3 glue_1.8.0 colorspace_2.1-1 htmltools_0.5.8.1 #> [13] ragg_1.3.3 sass_0.4.9 scales_1.3.0 rmarkdown_2.29 #> [17] grid_4.4.2 tibble_3.2.1 evaluate_1.0.3 munsell_0.5.1 #> [21] jquerylib_0.1.4 fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4 #> [25] compiler_4.4.2 dplyr_1.1.4 fs_1.6.5 pkgconfig_2.0.3 #> [29] farver_2.1.2 systemfonts_1.2.0 digest_0.6.37 R6_2.5.1 #> [33] tidyselect_1.2.1 pillar_1.10.1 magrittr_2.0.3 bslib_0.8.0 #> [37] withr_3.0.2 tools_4.4.2 gtable_0.3.6 pkgdown_2.1.1 #> [41] cachem_1.1.0 desc_1.4.3"},{"path":"https://yunuuuu.github.io/ggalign/dev/articles/benchmarks.html","id":"compared-with-other-packages","dir":"Articles","previous_headings":"","what":"Compared with other packages","title":"Benchmarks","text":"simple heatmap. heatmap dendrogram","code":"bench::mark( \"heatmap()\" = { pdf(NULL) heatmap(mat, Rowv = NA, Colv = NA) dev.off() NULL }, \"heatmap.2()\" = { pdf(NULL) heatmap.2(mat, dendrogram = \"none\", trace = \"none\") dev.off() NULL }, \"Heatmap()\" = { pdf(NULL) draw(Heatmap(mat, cluster_rows = FALSE, cluster_columns = FALSE, use_raster = TRUE )) dev.off() NULL }, \"pheatmap()\" = { pdf(NULL) pheatmap(mat, cluster_rows = FALSE, cluster_cols = FALSE) dev.off() NULL }, \"ggalign()\" = { pdf(NULL) print(ggheatmap(mat, filling = \"raster\")) dev.off() NULL } ) #> Warning: Some expressions had a GC in every iteration; so filtering is #> disabled. #> # A tibble: 5 × 6 #> expression min median `itr/sec` mem_alloc `gc/sec` #> #> 1 heatmap() 145.63ms 153.56ms 6.41 139.11MB 3.20 #> 2 heatmap.2() 2.24s 2.24s 0.446 224.23MB 0.891 #> 3 Heatmap() 4.36s 4.36s 0.230 792.59MB 2.98 #> 4 pheatmap() 644.69ms 644.69ms 1.55 124.1MB 3.10 #> 5 ggalign() 2.46s 2.46s 0.407 2.51GB 10.2 bench::mark( \"heatmap()\" = { pdf(NULL) heatmap(mat) dev.off() NULL }, \"heatmap.2()\" = { pdf(NULL) heatmap.2(mat, trace = \"none\") dev.off() NULL }, \"Heatmap()\" = { pdf(NULL) draw(Heatmap(mat, row_dend_reorder = FALSE, column_dend_reorder = FALSE, use_raster = TRUE )) dev.off() NULL }, \"pheatmap()\" = { pdf(NULL) pheatmap(mat) dev.off() NULL }, \"ggalign()\" = { pdf(NULL) print(ggheatmap(mat, filling = \"raster\") + anno_top() + align_dendro() + anno_right() + align_dendro()) dev.off() NULL } ) #> Warning: Some expressions had a GC in every iteration; so filtering is #> disabled. #> # A tibble: 5 × 6 #> expression min median `itr/sec` mem_alloc `gc/sec` #> #> 1 heatmap() 2.63s 2.63s 0.380 173.72MB 1.14 #> 2 heatmap.2() 3.14s 3.14s 0.318 223.41MB 0.954 #> 3 Heatmap() 5.43s 5.43s 0.184 1.51GB 1.47 #> 4 pheatmap() 2.27s 2.27s 0.441 177.53MB 0.881 #> 5 ggalign() 4.86s 4.86s 0.206 2.58GB 4.11"},{"path":"https://yunuuuu.github.io/ggalign/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Yun Peng. Author, maintainer. Shixiang Wang. Author.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Peng Y, Wang S (2025). ggalign: 'ggplot2' Extension Consistent Axis Alignment. R package version 0.0.5.9000, https://yunuuuu.github.io/ggalign/, https://github.com/Yunuuuu/ggalign.","code":"@Manual{, title = {ggalign: A 'ggplot2' Extension for Consistent Axis Alignment}, author = {Yun Peng and Shixiang Wang}, year = {2025}, note = {R package version 0.0.5.9000, https://yunuuuu.github.io/ggalign/}, url = {https://github.com/Yunuuuu/ggalign}, }"},{"path":"https://yunuuuu.github.io/ggalign/dev/index.html","id":"ggalign-","dir":"","previous_headings":"","what":"A ggplot2 Extension for Consistent Axis Alignment","title":"A ggplot2 Extension for Consistent Axis Alignment","text":"package extends ggplot2 providing advanced tools aligning organizing multiple plots, particularly automatically reorder observations, dendrogram. offers fine control layout adjustment plot annotations, enabling create complex, publication-quality visualizations still using familiar grammar ggplot2.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/index.html","id":"why-use-ggalign","dir":"","previous_headings":"","what":"Why use ggalign?","title":"A ggplot2 Extension for Consistent Axis Alignment","text":"ggalign focuses aligning observations across multiple plots. leverages \"number observations\" vctrs package NROW() function maintain consistency plot organization. ’ve ever struggled aligning plots self-contained ordering (like dendrogram), applying consistent grouping ordering across multiple plots (e.g., k-means clustering), ggalign designed make easier. package integrates seamlessly ggplot2, providing flexibility use geoms, scales, components complex visualizations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"A ggplot2 Extension for Consistent Axis Alignment","text":"can install ggalign CRAN using: Alternatively, install development version r-universe : GitHub :","code":"install.packages(\"ggalign\") install.packages(\"ggalign\", repos = c(\"https://yunuuuu.r-universe.dev\", \"https://cloud.r-project.org\") ) # install.packages(\"remotes\") remotes::install_github(\"Yunuuuu/ggalign\")"},{"path":"https://yunuuuu.github.io/ggalign/dev/index.html","id":"learning-ggalign","dir":"","previous_headings":"","what":"Learning ggalign","title":"A ggplot2 Extension for Consistent Axis Alignment","text":"complete tutorial available : https://yunuuuu.github.io/ggalign-book/ full reference documentation, visit: https://yunuuuu.github.io/ggalign/","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/index.html","id":"acknowledgements","dir":"","previous_headings":"","what":"Acknowledgements","title":"A ggplot2 Extension for Consistent Axis Alignment","text":"like express sincere gratitude contributors ggplot2 project providing powerful flexible framework data visualization R. work laid foundation functionality design package. also like thank patchwork project, core coding plot composer adapted. patchwork library provided useful mechanism combining aligning plots, modified suit needs package. Without contributions open-source projects, package possible. Additionally, like extend heartfelt thanks @teunbrand, fulfilled numerous feature requests, assisted integration new functions ggplot2.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/LayoutProto-class.html","id":null,"dir":"Reference","previous_headings":"","what":"A Layout object — LayoutProto-class","title":"A Layout object — LayoutProto-class","text":"Layout object defines place plots.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/active.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Adding Context Settings — active","title":"Plot Adding Context Settings — active","text":"settings control behavior plot added layout, well arrangement individual plot areas within layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/active.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Adding Context Settings — active","text":"","code":"active(order = waiver(), use = waiver(), name = waiver())"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/active.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Adding Context Settings — active","text":"order integer specifying order plot area within layout. use logical (TRUE/FALSE) indicating whether set active context current plot added layout. TRUE, subsequent ggplot elements applied plot. name string specifying plot's name, useful switching active contexts argument functions like quad_anno()/stack_switch().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/active.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot Adding Context Settings — active","text":"default, active context set functions add plot areas. allows ggplot2 elements-geoms, stats, scales, themes- seamlessly added current plot area. default ordering plot areas top bottom left right, depending layout orientation. However, users can customize order using order argument.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a New align Object — align","title":"Create a New align Object — align","text":"Align object interacts Layout object reorder split observations , cases, add plot components Layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a New align Object — align","text":"","code":"align( align, data = NULL, ..., plot = NULL, size = NULL, schemes = NULL, no_axes = NULL, active = NULL, call = caller_call() )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a New align Object — align","text":"align Align object. data following options can used: NULL: data set. waiver(): Inherits data layout matrix. function (including purrr-like lambda syntax): Applied layout matrix transform data use. transform final plot data, please use scheme_data(). matrix, data.frame, atomic vector. ... Additional fields passed align object. plot ggplot object. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. schemes Options schemes: NULL: Used align add plot. waiver(): Try infer schemes based data. no_axes Logical; TRUE, removes axes elements alignment axis using theme_no_axes(). default, use option- \"ggalign.align_no_axes\". active active() object defines context settings added layout. call call used construct Align object, reporting messages.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a New align Object — align","text":"new ggalign_plot object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a New align Object — align","text":"Align* objects just ggproto() object, descended top-level Align, implements various methods fields. create new type Align* object, typically want override one following: setup_params: Prepare parameter check parameters used plot. setup_data: Prepare data used plot. compute: method used compute statistics. align: method used group observations panel reorder observations. draw: method used draw plot. Must return ggplot object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Create a New align Object — align","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a New align Object — align","text":"","code":"align_dendro() #> #> plot: yes #> reorder: yes #> split: no"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot dendrogram tree — align_dendro","title":"Plot dendrogram tree — align_dendro","text":"Plot dendrogram tree","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot dendrogram tree — align_dendro","text":"","code":"align_dendro( mapping = aes(), ..., distance = \"euclidean\", method = \"complete\", use_missing = \"pairwise.complete.obs\", reorder_dendrogram = FALSE, merge_dendrogram = FALSE, reorder_group = FALSE, k = NULL, h = NULL, cutree = NULL, plot_dendrogram = TRUE, plot_cut_height = NULL, root = NULL, center = FALSE, type = \"rectangle\", size = NULL, data = NULL, no_axes = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot dendrogram tree — align_dendro","text":"mapping Default list aesthetic mappings use plot. specified, must supplied layer added plot. ... Additional arguments passed geom_segment(). distance string distance measure used. must one \"euclidean\", \"maximum\", \"manhattan\", \"canberra\", \"binary\" \"minkowski\". Correlation coefficient can also used, including \"pearson\", \"spearman\" \"kendall\". way, 1 - cor used distance. addition, can also provide dist object directly function return dist object. Use NULL, want calculate distance. method string agglomeration method used. (unambiguous abbreviation ) one \"ward.D\", \"ward.D2\", \"single\", \"complete\", \"average\" (= UPGMA), \"mcquitty\" (= WPGMA), \"median\" (= WPGMC) \"centroid\" (= UPGMC). can also provide function accepts calculated distance (input matrix distance NULL) returns hclust object. Alternative, can supply object can coerced hclust. use_missing optional character string giving method computing covariances presence missing values. must (abbreviation ) one strings \"everything\", \".obs\", \"complete.obs\", \"na..complete\", \"pairwise.complete.obs\". used distance correlation coefficient string. reorder_dendrogram single boolean value indicating whether reorder dendrogram based means. Alternatively, can provide custom function accepts hclust object data used generate tree, returning either hclust dendrogram object. Default FALSE. merge_dendrogram single boolean value, indicates whether merge multiple dendrograms, used previous groups established. Default: FALSE. reorder_group single boolean value, indicates whether Hierarchical Clustering groups, used previous groups established. Default: FALSE. k integer scalar indicates desired number groups. h numeric scalar indicates heights tree cut. cutree function used cut hclust tree. accept four arguments: hclust tree object, distance (applicable method string function performing hierarchical clustering), k (number clusters), h (height cut tree). default, cutree() used. plot_dendrogram boolean value indicates whether plot dendrogram tree. plot_cut_height boolean value indicates whether plot cut height. root length one string numeric indicates root branch. center boolean value. TRUE, nodes plotted centered respect leaves/tips branch. Otherwise (default), plot middle direct child nodes. type string indicates plot type, \"rectangle\" \"triangle\". size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. data matrix-like object. default, inherits layout matrix. no_axes Logical; TRUE, removes axes elements alignment axis using theme_no_axes(). default, use option- \"ggalign.align_no_axes\". active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Plot dendrogram tree — align_dendro","text":"align_dendro initializes ggplot data mapping. internal ggplot object always use default mapping aes(x = .data$x, y = .data$y). default ggplot data node coordinates edge data attached ggalign attribute, addition, geom_segment layer data frame edge coordinates added plot_dendrogram = TRUE. See fortify_data_frame.dendrogram() details.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Plot dendrogram tree — align_dendro","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot dendrogram tree — align_dendro","text":"","code":"# align_dendro will always add a plot area ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + align_dendro() #> → heatmap built with `geom_tile()` ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + align_dendro(k = 3L) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_group.html","id":null,"dir":"Reference","previous_headings":"","what":"Group and align observations based on a group vector — align_group","title":"Group and align observations based on a group vector — align_group","text":"Splits observations groups, slice ordering based group levels.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_group.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Group and align observations based on a group vector — align_group","text":"","code":"align_group(group, active = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_group.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Group and align observations based on a group vector — align_group","text":"group character define groups observations. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_group.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Group and align observations based on a group vector — align_group","text":"","code":"set.seed(1L) small_mat <- matrix(rnorm(81), nrow = 9) ggheatmap(small_mat) + anno_top() + align_group(sample(letters[1:4], ncol(small_mat), replace = TRUE)) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_hclust.html","id":null,"dir":"Reference","previous_headings":"","what":"Reorder or Group observations based on hierarchical clustering — align_hclust","title":"Reorder or Group observations based on hierarchical clustering — align_hclust","text":"function aligns observations within layout according hierarchical clustering tree, enabling reordering grouping elements based clustering results.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_hclust.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reorder or Group observations based on hierarchical clustering — align_hclust","text":"","code":"align_hclust( distance = \"euclidean\", method = \"complete\", use_missing = \"pairwise.complete.obs\", reorder_dendrogram = FALSE, reorder_group = FALSE, k = NULL, h = NULL, cutree = NULL, data = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_hclust.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reorder or Group observations based on hierarchical clustering — align_hclust","text":"distance string distance measure used. must one \"euclidean\", \"maximum\", \"manhattan\", \"canberra\", \"binary\" \"minkowski\". Correlation coefficient can also used, including \"pearson\", \"spearman\" \"kendall\". way, 1 - cor used distance. addition, can also provide dist object directly function return dist object. Use NULL, want calculate distance. method string agglomeration method used. (unambiguous abbreviation ) one \"ward.D\", \"ward.D2\", \"single\", \"complete\", \"average\" (= UPGMA), \"mcquitty\" (= WPGMA), \"median\" (= WPGMC) \"centroid\" (= UPGMC). can also provide function accepts calculated distance (input matrix distance NULL) returns hclust object. Alternative, can supply object can coerced hclust. use_missing optional character string giving method computing covariances presence missing values. must (abbreviation ) one strings \"everything\", \".obs\", \"complete.obs\", \"na..complete\", \"pairwise.complete.obs\". used distance correlation coefficient string. reorder_dendrogram single boolean value indicating whether reorder dendrogram based means. Alternatively, can provide custom function accepts hclust object data used generate tree, returning either hclust dendrogram object. Default FALSE. reorder_group single boolean value, indicates whether Hierarchical Clustering groups, used previous groups established. Default: FALSE. k integer scalar indicates desired number groups. h numeric scalar indicates heights tree cut. cutree function used cut hclust tree. accept four arguments: hclust tree object, distance (applicable method string function performing hierarchical clustering), k (number clusters), h (height cut tree). default, cutree() used. data matrix-like object. default, inherits layout matrix. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_hclust.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Reorder or Group observations based on hierarchical clustering — align_hclust","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_hclust.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reorder or Group observations based on hierarchical clustering — align_hclust","text":"","code":"# align_hclust won't add a dendrogram ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + align_hclust(k = 3L) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_kmeans.html","id":null,"dir":"Reference","previous_headings":"","what":"Split observations by k-means clustering groups. — align_kmeans","title":"Split observations by k-means clustering groups. — align_kmeans","text":"Aligns groups observations based k-means clustering, enabling observation splits cluster groups.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_kmeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split observations by k-means clustering groups. — align_kmeans","text":"","code":"align_kmeans(..., data = NULL, active = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_kmeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split observations by k-means clustering groups. — align_kmeans","text":"... Arguments passed stats::kmeans iter.max maximum number iterations allowed. nstart centers number, many random sets chosen? algorithm character: may abbreviated. Note \"Lloyd\" \"Forgy\" alternative names one algorithm. trace logical integer number, currently used default method (\"Hartigan-Wong\"): positive (true), tracing information progress algorithm produced. Higher values may produce tracing information. data numeric matrix used k-means. default, inherit layout matrix. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_kmeans.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Split observations by k-means clustering groups. — align_kmeans","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_kmeans.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split observations by k-means clustering groups. — align_kmeans","text":"","code":"ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + align_kmeans(3L) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_order.html","id":null,"dir":"Reference","previous_headings":"","what":"Order observations based on weights — align_order","title":"Order observations based on weights — align_order","text":"Ordering observations based summary weights specified ordering character integer index.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_order.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Order observations based on weights — align_order","text":"","code":"align_order( weights = rowMeans, ..., reverse = FALSE, strict = TRUE, data = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_order.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Order observations based on weights — align_order","text":"weights summary function accepts data returns weights observations. Alternatively, can provide ordering index either integer character. Since characters designated character indices, wish specify function name string, must enclose (). ... Additional arguments passed function provided weights argument. reverse boolean value. sort order reverse? strict boolean value indicates whether order strict. previous groups established, strict FALSE, reorder observations group. data matrix, data frame, atomic vector used input weights function. Alternatively, can specify function (including purrr-like lambda syntax) applied layout matrix, transforming necessary weight calculations. default, inherit layout matrix. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_order.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Order observations based on weights — align_order","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_order.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Order observations based on weights — align_order","text":"","code":"ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_left() + align_order(I(\"rowMeans\")) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_panel.html","id":null,"dir":"Reference","previous_headings":"","what":"Create ggplot object with layout panel data — align_panel","title":"Create ggplot object with layout panel data — align_panel","text":"function deprecated realised special case ggalign() function. Please use ggalign(data = NULL) instead.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_panel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create ggplot object with layout panel data — align_panel","text":"","code":"align_panel(...) ggpanel(...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Phylogenetics tree — align_phylo","title":"Plot Phylogenetics tree — align_phylo","text":"Plot Phylogenetics tree","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Phylogenetics tree — align_phylo","text":"","code":"align_phylo( phylo, ..., ladderize = NULL, type = \"rectangle\", center = FALSE, tree_type = NULL, no_axes = NULL, active = NULL, size = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Phylogenetics tree — align_phylo","text":"phylo phylo object. ... Additional arguments passed geom_segment(). ladderize single string \"left\" \"right\", indicating whether ladderize tree. Ladderizing arranges tree smallest clade positioned \"right\" \"left\". default, NULL means tree ladderized. type string indicates plot type, \"rectangle\" \"triangle\". center boolean value. TRUE, nodes plotted centered respect leaves/tips branch. Otherwise (default), plot middle direct child nodes. tree_type single string, one \"phylogram\" \"cladogram\", indicating type tree. phylogram: Represents phylogenetic tree branch lengths indicate evolutionary distance time. cladogram: Represents tree branch lengths used, branches reflect evolutionary time. Usually, need modify . no_axes Logical; TRUE, removes axes elements alignment axis using theme_no_axes(). default, use option- \"ggalign.align_no_axes\". active active() object defines context settings added layout. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange multiple plots into a grid — align_plots","title":"Arrange multiple plots into a grid — align_plots","text":"Arrange multiple plots grid","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange multiple plots into a grid — align_plots","text":"","code":"align_plots( ..., ncol = NULL, nrow = NULL, byrow = TRUE, widths = NA, heights = NA, design = NULL, guides = waiver(), theme = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange multiple plots into a grid — align_plots","text":"... list plots, ususally ggplot object. Use NULL indicate empty spacer. ncol, nrow dimensions grid create - NULL use logic facet_wrap() set dimensions byrow FALSE plots filled column-major order. widths, heights relative widths heights column row grid. get repeated match dimensions grid. special value NA behave 1null unit unless fixed aspect plot inserted case allow dimension expand contract match aspect ratio content. design Specification location areas layout. Can either specified text string concatenating calls area() together. guides string one \"t\", \"l\", \"b\", \"r\" indicating side guide legends collected. Defaults waiver(), inherits parent layout. parent layout, NULL provided, guides collected. theme theme() object used customize various elements plot, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange multiple plots into a grid — align_plots","text":"alignpatches object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange multiple plots into a grid — align_plots","text":"","code":"# directly copied from patchwork p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p3 <- ggplot(mtcars) + geom_bar(aes(gear)) + facet_wrap(~cyl) p4 <- ggplot(mtcars) + geom_bar(aes(carb)) p5 <- ggplot(mtcars) + geom_violin(aes(cyl, mpg, group = cyl)) # Either add the plots as single arguments align_plots(p1, p2, p3, p4, p5) # Or use bang-bang-bang to add a list align_plots(!!!list(p1, p2, p3), p4, p5) # Match plots to areas by name design <- \"#BB AA#\" align_plots(B = p1, A = p2, design = design) # Compare to not using named plot arguments align_plots(p1, p2, design = design)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":null,"dir":"Reference","previous_headings":"","what":"Reorders layout observations based on specific statistics. — align_reorder","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"Reorders layout observations based specific statistics.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"","code":"align_reorder( stat, ..., reverse = FALSE, strict = TRUE, data = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"stat statistical function accepts data returns statistic, call order2() extract ordering information. ... Additional arguments passed function provided stat argument. reverse boolean value. sort order reverse? strict boolean value indicates whether order strict. previous groups established, strict FALSE, reorder observations group. data matrix, data frame, atomic vector used input stat function. Alternatively, can specify function (including purrr-like lambda syntax) applied layout matrix, transforming necessary statistic calculations. default, inherit layout matrix. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"align_reorder() function differs align_order() weights argument align_order() must return atomic weights observation. contrast, stat argument align_reorder() can return complex structures, hclust dendrogram, among others. Typically, can achieve functionality align_reorder() using align_order() manually extracting ordering information statistic.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"","code":"ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_left() + align_reorder(hclust2) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare plots to be aligned with align_plots — alignpatch","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"Prepare plots aligned align_plots","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"","code":"alignpatch(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"x plot object prepared alignment.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"Patch object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"ggalign implement alignpatch method following objects: ggplot alignpatches wrapped_plot patch wrapped_patch spacer","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"","code":"alignpatch(ggplot()) #> #> add_background: function #> add_plot: function #> align_border: function #> align_free_border: function #> align_panel_sizes: function #> collect_guides: function #> free_border: function #> free_lab: function #> get_sizes: function #> patch_gtable: function #> plot: gg, ggplot #> respect: function #> set_guides: function #> set_theme: function #> split_gt: function #> super: "},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the plotting areas in align_plots — area","title":"Define the plotting areas in align_plots — area","text":"small helper used specify single area rectangular grid contain plot. Objects constructed area() can concatenated together c() order specify multiple areas.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the plotting areas in align_plots — area","text":"","code":"area(t, l, b = t, r = l)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the plotting areas in align_plots — area","text":"t, b top bottom bounds area grid l, r left right bounds area int grid","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define the plotting areas in align_plots — area","text":"ggalign_area object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Define the plotting areas in align_plots — area","text":"grid areas specified reference enumerate rows top bottom, coloumns left right. means t l always less equal b r respectively. Instead specifying area placement combination area() calls, possible instead pass single string equivalent ","code":"areas <- c(area(1, 1, 2, 1), area(2, 3, 3, 3)) areas < -\"A## A#B ##B\""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define the plotting areas in align_plots — area","text":"","code":"p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p3 <- ggplot(mtcars) + geom_bar(aes(gear)) + facet_wrap(~cyl) layout <- c( area(1, 1), area(1, 3, 3), area(3, 1, 3, 2) ) #> Error in vec_slice(vec_data(x), i): Can't use character names to index an unnamed vector. # Show the layout to make sure it looks as it should plot(layout) #> Error in curve(expr = x, from = from, to = to, xlim = xlim, ylab = ylab, ...): 'expr' did not evaluate to an object of length 'n' # Apply it to a alignpatches align_plots(p1, p2, p3, design = layout) #> Error in as_areas(design): Cannot convert a function into a design area"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cash-LayoutProto-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset a Layout object — $,LayoutProto-method","title":"Subset a Layout object — $,LayoutProto-method","text":"Used ggplot_build ggsave","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cash-LayoutProto-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset a Layout object — $,LayoutProto-method","text":"","code":"# S4 method for class 'LayoutProto' x$name"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cash-LayoutProto-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset a Layout object — $,LayoutProto-method","text":"x Layout object name string slot name Layout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cash-LayoutProto-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset a Layout object — $,LayoutProto-method","text":"slot value.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange plots in a circular layout — circle_layout","title":"Arrange plots in a circular layout — circle_layout","text":"limits provided, continuous variable required aligned direction specified (circle_continuous). Otherwise, discrete variable required aligned (circle_discrete).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange plots in a circular layout — circle_layout","text":"","code":"circle_layout( data = NULL, ..., radial = NULL, direction = \"outward\", limits = waiver(), theme = NULL ) circle_discrete( data = NULL, ..., radial = NULL, direction = \"outward\", theme = NULL ) circle_continuous( data = NULL, ..., radial = NULL, direction = \"outward\", limits = NULL, theme = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange plots in a circular layout — circle_layout","text":"data Default dataset use layout. specified, must supplied plot added layout: limits provided, fortify_matrix() used get matrix. limits specified, fortify_data_frame() used get data frame. Note data matrix, automatically converted long-formatted data frame, differs ggplot2's behavior. ... Additional arguments passed fortify_data_frame() fortify_matrix(). radial coord_radial() object defines global parameters coord_radial across plots layout. parameters start, end, direction, expand inherited applied uniformly plots within layout. parameters theta r.axis.inside always ignored set \"x\" TRUE, respectively, plots. direction single string \"inward\" \"outward\", indicating direction plot added. outward: plot added inner outer. inward: plot added outer inner. limits continuous_limits() object specifying left/lower limit right/upper limit scale. Used align continuous axis. theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange plots in a circular layout — circle_layout","text":"CircleLayout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange plots in a circular layout — circle_layout","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) rownames(small_mat) <- paste0(\"row\", seq_len(nrow(small_mat))) colnames(small_mat) <- paste0(\"column\", seq_len(ncol(small_mat))) # circle_layout # same for circle_discrete() circle_layout(small_mat) + ggalign() + geom_tile(aes(y = .column_index, fill = value)) + scale_fill_viridis_c() + align_dendro(aes(color = branch), k = 3L) + scale_color_brewer(palette = \"Dark2\") # same for circle_continuous() circle_layout(mpg, limits = continuous_limits(c(3, 5))) + ggalign(mapping = aes(displ, hwy, colour = class)) + geom_point(size = 2) + ggalign(mapping = aes(displ, hwy, colour = class)) + geom_point(size = 2) & scale_color_brewer(palette = \"Dark2\") & theme_bw() # circle_discrete() # direction outward circle_discrete(small_mat) + align_dendro(aes(color = branch), k = 3L) + scale_color_brewer(palette = \"Dark2\") + ggalign() + geom_tile(aes(y = .column_index, fill = value)) + scale_fill_viridis_c() # direction inward circle_discrete(small_mat, direction = \"inward\") + ggalign() + geom_tile(aes(y = .column_index, fill = value)) + scale_fill_viridis_c() + align_dendro(aes(color = branch), k = 3L) + scale_color_brewer(palette = \"Dark2\") # circle_continuous() circle_continuous(mpg, limits = continuous_limits(c(3, 5))) + ggalign(mapping = aes(displ, hwy, colour = class)) + geom_point(size = 2) + ggalign(mapping = aes(displ, hwy, colour = class)) + geom_point(size = 2) & scale_color_brewer(palette = \"Dark2\") & theme_bw()"},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_switch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the active context of circle layout — circle_switch","text":"","code":"circle_switch(radial = waiver(), direction = NULL, what = waiver(), ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_switch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the active context of circle layout — circle_switch","text":"radial coord_radial() object defines global parameters coord_radial across plots layout. parameters start, end, direction, expand inherited applied uniformly plots within layout. parameters theta r.axis.inside always ignored set \"x\" TRUE, respectively, plots. direction single string \"inward\" \"outward\", indicating direction plot added. outward: plot added inner outer. inward: plot added outer inner. get activated circle_layout()? single number string plot elements layout. NULL, remove active context. ... dots future extensions must empty.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_switch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the active context of circle layout — circle_switch","text":"circle_switch object can added circle_layout().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_switch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine the active context of circle layout — circle_switch","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) rownames(small_mat) <- paste0(\"row\", seq_len(nrow(small_mat))) colnames(small_mat) <- paste0(\"column\", seq_len(ncol(small_mat))) circle_discrete(small_mat) + ggalign() + geom_tile(aes(y = .column_index, fill = value)) + scale_fill_viridis_c() + align_dendro(aes(color = branch), k = 3L) + scale_color_brewer(palette = \"Dark2\")"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/continuous_limits.html","id":null,"dir":"Reference","previous_headings":"","what":"Set continuous limits for the layout — continuous_limits","title":"Set continuous limits for the layout — continuous_limits","text":"align continuous axes, important keep limits consistent across plots layout. can set limits passing function directly limits xlim/ylim argument, using ... . Alternatively, can add continuous_limits() object layout. quad_layout() function, must specify x/y arguments. layouts, pass limits using ... directly.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/continuous_limits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set continuous limits for the layout — continuous_limits","text":"","code":"continuous_limits(..., x = waiver(), y = waiver())"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/continuous_limits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set continuous limits for the layout — continuous_limits","text":"... list two numeric values, specifying left/lower limit right/upper limit scale. x, y ..., specifically quad_layout().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_link.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a plot to connect selected observations — cross_link","title":"Add a plot to connect selected observations — cross_link","text":"Add plot connect selected observations","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_link.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a plot to connect selected observations — cross_link","text":"","code":"cross_link( link, data = waiver(), ..., on_top = TRUE, obs_size = 1, inherit_index = NULL, inherit_panel = NULL, inherit_nobs = NULL, size = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_link.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a plot to connect selected observations — cross_link","text":"link link_draw() object defines draw links, link_line(). data dataset use layout. default, fortify_matrix() convert data matrix. argument allows change layout data. specified, original data used. ... Additional arguments passed fortify_matrix(). on_top boolean value indicating whether draw link top plot panel (TRUE) (FALSE). obs_size single numeric value indicates size single observation, ranging (0, 1]. inherit_index boolean value indicating whether inherit ordering index. TRUE, match layout ordering index data names. inherit_panel boolean value indicating whether inherit panel group. TRUE, match layout panel data names. inherit_nobs boolean value indicating whether inherit number observations (nobs). TRUE, data input must compatible layout data. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_link.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 Specification","title":"Add a plot to connect selected observations — cross_link","text":"cross_link function initializes ggplot object initialize data. Using scheme_data() change internal data needed.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_mark.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a plot to annotate observations — cross_mark","title":"Add a plot to annotate observations — cross_mark","text":"Add plot annotate observations","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_mark.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a plot to annotate observations — cross_mark","text":"","code":"cross_mark( mark, data = waiver(), ..., obs_size = 1, inherit_index = NULL, inherit_panel = NULL, inherit_nobs = NULL, size = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_mark.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a plot to annotate observations — cross_mark","text":"mark mark_draw() object define draw links. Like mark_line(), mark_tetragon(). Note names pair links used define panel names must unique. data dataset use layout. default, fortify_matrix() convert data matrix. argument allows change layout data. specified, original data used. ... Additional arguments passed fortify_matrix(). obs_size single numeric value indicates size single observation, ranging (0, 1]. inherit_index boolean value indicating whether inherit ordering index. TRUE, match layout ordering index data names. inherit_panel boolean value indicating whether inherit panel group. TRUE, match layout panel data names. inherit_nobs boolean value indicating whether inherit number observations (nobs). TRUE, data input must compatible layout data. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_mark.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 Specification","title":"Add a plot to annotate observations — cross_mark","text":"cross_mark function initializes ggplot object. underlying data contains following columns: .panel: panel aligned axis. means x-axis vertical stack layout (including top bottom annotation), y-axis horizontal stack layout (including left right annotation). .names (vec_names()) .index (vec_size()/NROW()): character names (applicable names exists) integer index original data. .hand: factor levels c(\"left\", \"right\") horizontal stack layouts, c(\"top\", \"bottom\") vertical stack layouts, indicating position linked observations. can use scheme_data() modify internal data needed.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_none.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset layout ordering and panel group — cross_none","title":"Reset layout ordering and panel group — cross_none","text":"Reset layout ordering panel group","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_none.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset layout ordering and panel group — cross_none","text":"","code":"cross_none( data = waiver(), ..., inherit_index = NULL, inherit_panel = NULL, inherit_nobs = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_none.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reset layout ordering and panel group — cross_none","text":"data dataset use layout. default, fortify_matrix() convert data matrix. argument allows change layout data. specified, original data used. ... Additional arguments passed fortify_matrix(). inherit_index boolean value indicating whether inherit ordering index. TRUE, match layout ordering index data names. inherit_panel boolean value indicating whether inherit panel group. TRUE, match layout panel data names. inherit_nobs boolean value indicating whether inherit number observations (nobs). TRUE, data input must compatible layout data.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-link_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the links to connect a pair of observations — .link_draw","title":"Define the links to connect a pair of observations — .link_draw","text":"base version link_draw(), optimized performance. function serves foundation building link_* functions manage drawing links pairs observations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-link_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the links to connect a pair of observations — .link_draw","text":"","code":".link_draw(.draw, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-link_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the links to connect a pair of observations — .link_draw","text":".draw function used draw links. function must return grob() object. function return valid grob, drawing occur. input data function list, item data frame containing coordinates pair observations. ... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-mark_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the links to connect the marked observations — .mark_draw","title":"Define the links to connect the marked observations — .mark_draw","text":"base version mark_draw, designed performance optimization. function used build mark_* functions manage drawing links marked observations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-mark_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the links to connect the marked observations — .mark_draw","text":"","code":".mark_draw(.draw, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-mark_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the links to connect the marked observations — .mark_draw","text":".draw function used draw links. function must return grob() object. function return valid grob, nothing drawn. input data function contains list, item list two data frames: one panel side coordinates (\"panel\") one marked observations coordinates (\"link\"). ... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Key glyphs for legends — draw_key_draw","title":"Key glyphs for legends — draw_key_draw","text":"geom associated function draws key geom needs displayed legend. functions called draw_key_*(), * stands name respective key glyph. key glyphs can customized individual geoms providing geom key_glyph argument. draw_key_draw function provides interface custom key glyphs used geom_draw().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Key glyphs for legends — draw_key_draw","text":"","code":"draw_key_draw(data, params, size)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Key glyphs for legends — draw_key_draw","text":"data single row data frame containing scaled aesthetics display key params list additional parameters supplied geom. size Width height key mm.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Key glyphs for legends — draw_key_draw","text":"grid grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Key glyphs for legends — draw_key_draw","text":"","code":"p <- ggplot(economics, aes(date, psavert, color = \"savings rate\")) # key glyphs can be specified by their name p + geom_line(key_glyph = \"timeseries\") # key glyphs can be specified via their drawing function p + geom_line(key_glyph = draw_key_rect)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw2.html","id":null,"dir":"Reference","previous_headings":"","what":"Key glyphs for legends — draw_key_draw2","title":"Key glyphs for legends — draw_key_draw2","text":"geom associated function draws key geom needs displayed legend. functions called draw_key_*(), * stands name respective key glyph. key glyphs can customized individual geoms providing geom key_glyph argument. draw_key_draw2 function provides interface custom key glyphs used geom_draw2().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Key glyphs for legends — draw_key_draw2","text":"","code":"draw_key_draw2(data, params, size)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Key glyphs for legends — draw_key_draw2","text":"data single row data frame containing scaled aesthetics display key params list additional parameters supplied geom. size Width height key mm.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Key glyphs for legends — draw_key_draw2","text":"grid grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Key glyphs for legends — draw_key_draw2","text":"","code":"p <- ggplot(economics, aes(date, psavert, color = \"savings rate\")) # key glyphs can be specified by their name p + geom_line(key_glyph = \"timeseries\") # key glyphs can be specified via their drawing function p + geom_line(key_glyph = draw_key_rect)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_curve.html","id":null,"dir":"Reference","previous_headings":"","what":"Theme curve elements — element_curve","title":"Theme curve elements — element_curve","text":"Draw curve.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_curve.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Theme curve elements — element_curve","text":"","code":"element_curve( colour = NULL, linewidth = NULL, linetype = NULL, lineend = NULL, color = NULL, curvature = NULL, angle = NULL, ncp = NULL, shape = NULL, arrow = NULL, arrow.fill = NULL, inherit.blank = FALSE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_curve.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Theme curve elements — element_curve","text":"colour, color Line/border colour. Color alias colour. linewidth Line/border size mm. linetype Line type. integer (0:8), name (blank, solid, dashed, dotted, dotdash, longdash, twodash), string even number (eight) hexadecimal digits give lengths consecutive positions string. lineend Line end Line end style (round, butt, square) curvature numeric value giving amount curvature. Negative values produce left-hand curves, positive values produce right-hand curves, zero produces straight line. angle numeric value 0 180, giving amount skew control points curve. Values less 90 skew curve towards start point values greater 90 skew curve towards end point. ncp number control points used draw curve. control points creates smoother curve. shape numeric vector values -1 1, control shape curve relative control points. See grid.xspline details. arrow list describing arrow heads place either end curve, produced arrow function. arrow.fill Fill colour arrows. inherit.blank element inherit existence element_blank among parents? TRUE existence blank element among parents cause element blank well. FALSE blank parent element ignored calculating final element state.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_curve.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Theme curve elements — element_curve","text":"element_curve object","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_polygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Theme Polygon elements — element_polygon","title":"Theme Polygon elements — element_polygon","text":"Draw polygon.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_polygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Theme Polygon elements — element_polygon","text":"","code":"element_polygon( fill = NULL, colour = NULL, linewidth = NULL, linetype = NULL, alpha = NULL, lineend = NULL, linejoin = NULL, linemitre = NULL, color = NULL, inherit.blank = FALSE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_polygon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Theme Polygon elements — element_polygon","text":"fill Fill colour. colour, color Line/border colour. Color alias colour. linewidth Line/border size mm. linetype Line type. integer (0:8), name (blank, solid, dashed, dotted, dotdash, longdash, twodash), string even number (eight) hexadecimal digits give lengths consecutive positions string. alpha transparency value 0 (transparent) 1 (opaque), parallel fill. lineend Line end Line end style (round, butt, square) linejoin Line join style (round, mitre, bevel). linemitre Line mitre limit (number greater 1). inherit.blank element inherit existence element_blank among parents? TRUE existence blank element among parents cause element blank well. FALSE blank parent element ignored calculating final element state.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_polygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Theme Polygon elements — element_polygon","text":"element_polygon object","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply a function to the fields of an element object — element_vec","title":"Apply a function to the fields of an element object — element_vec","text":"element object, fields vectorized, others . function allows apply function vectorized fields. following helper functions available: element_rep: Applies rep(). element_rep_len: Applies rep_len(). element_vec_recycle: Applies vec_recycle(). element_vec_rep: Applies vec_rep(). element_vec_rep_each: Applies vec_rep_each(). element_vec_slice: Applies vec_slice().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply a function to the fields of an element object — element_vec","text":"","code":"element_vec(.el, .fn, ...) element_rep(.el, ...) element_rep_len(.el, length.out, ...) element_vec_recycle(.el, size, ...) element_vec_rep(.el, times, ...) element_vec_rep_each(.el, times, ...) element_vec_slice(.el, i, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply a function to the fields of an element object — element_vec","text":".el element object. .fn function applied vectorized fields element object. ... Additional arguments passed fn. length.Non-negative integer. desired length output vector. inputs coerced double vector first element taken. Ignored NA invalid. size Desired output size. times vec_rep(), single integer number times repeat entire vector. vec_rep_each(), integer vector number times repeat element x. times recycled size x. integer, character logical vector specifying locations names observations get/set. Specify TRUE index elements (x[]), NULL, FALSE integer() index none (x[NULL]).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.character.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame.character","title":"Build a data frame — fortify_data_frame.character","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame.character","text":"","code":"# S3 method for class 'character' fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL) # S3 method for class 'numeric' fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL) # S3 method for class 'logical' fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL) # S3 method for class 'complex' fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame.character","text":"data object converted data frame. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame.character","text":"data frame following columns: .names: names vector (applicable names exist). value: actual value vector.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.default.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame.default","title":"Build a data frame — fortify_data_frame.default","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.default.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame.default","text":"","code":"# Default S3 method fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.default.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame.default","text":"data object converted data frame. ... Additional arguments passed fortify(). data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.default.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame.default","text":"data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.default.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build a data frame — fortify_data_frame.default","text":"default, calls fortify() build data frame.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame.dendrogram","title":"Build a data frame — fortify_data_frame.dendrogram","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame.dendrogram","text":"","code":"# S3 method for class 'dendrogram' fortify_data_frame( data, ..., priority = \"right\", center = FALSE, type = \"rectangle\", leaf_pos = NULL, leaf_braches = NULL, reorder_branches = TRUE, branch_gap = NULL, root = NULL, double = TRUE, data_arg = caller_arg(data), call = NULL ) # S3 method for class 'hclust' fortify_data_frame(data, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame.dendrogram","text":"data hclust dendrogram object. ... Additional arguments passed dendrogram method. priority string \"left\" \"right\". draw right left, left override right, take \"left\" priority. draw left right, right override left, take \"right\" priority. used align_dendro() provide support facet operation ggplot2. center boolean value. TRUE, nodes plotted centered respect leaves/tips branch. Otherwise (default), plot middle direct child nodes. type string indicates plot type, \"rectangle\" \"triangle\". leaf_pos x-coordinates leaf node. Must length number observations tree. leaf_braches Branches leaf node. Must length number observations tree. Usually come cutree. reorder_branches single boolean value, indicates whether reorder provided leaf_braches based actual index. branch_gap single numeric value indicates gap different branches. root length one string numeric indicates root branch. double single logical value indicating whether horizontal lines doubled segments span multiple branches. TRUE, horizontal lines repeated branch segment spans. FALSE, one horizontal line drawn. used align_dendro() provide support facet operation ggplot2. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame.dendrogram","text":"data frame node coordinates: .panel: Similar panel column, always give correct branch usage ggplot facet. .index: original index tree node label: node label text x y: x-axis y-axis coordinates node branch: branch node . can use column color different groups. panel: panel node , split plot panel using facet_grid, column show panel node . Note: nodes may fall outside panel (two panels), possible NA values column. leaf: logical value indicates whether node leaf.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a data frame — fortify_data_frame.dendrogram","text":"edge: data frame edge coordinates: .panel: Similar panel column, always give correct branch usage ggplot facet. x y: x-axis y-axis coordinates start node edge. xend yend: x-axis y-axis coordinates terminal node edge. branch: branch edge . can use column color different groups. panel1 panel2: panel1 panel2 columns functionality panel, specifically edge data correspond nodes edge.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Build a data frame — fortify_data_frame.dendrogram","text":"","code":"fortify_data_frame(hclust(dist(USArrests), \"ave\")) #> .index label x y branch leaf panel .panel #> 1 9 Florida 1.000000 0.000000 root TRUE #> 2 33 North Carolina 2.000000 0.000000 root TRUE #> 3 NA 1.500000 38.527912 root FALSE #> 4 5 California 3.000000 0.000000 root TRUE #> 5 20 Maryland 4.000000 0.000000 root TRUE #> 6 3 Arizona 5.000000 0.000000 root TRUE #> 7 31 New Mexico 6.000000 0.000000 root TRUE #> 8 NA 5.500000 13.896043 root FALSE #> 9 NA 4.750000 15.453120 root FALSE #> 10 NA 3.875000 28.012211 root FALSE #> 11 8 Delaware 7.000000 0.000000 root TRUE #> 12 1 Alabama 8.000000 0.000000 root TRUE #> 13 18 Louisiana 9.000000 0.000000 root TRUE #> 14 NA 8.500000 15.454449 root FALSE #> 15 NA 7.750000 16.891499 root FALSE #> 16 13 Illinois 10.000000 0.000000 root TRUE #> 17 32 New York 11.000000 0.000000 root TRUE #> 18 NA 10.500000 6.236986 root FALSE #> 19 22 Michigan 12.000000 0.000000 root TRUE #> 20 28 Nevada 13.000000 0.000000 root TRUE #> 21 NA 12.500000 13.297368 root FALSE #> 22 NA 11.500000 18.417331 root FALSE #> 23 NA 9.625000 26.363428 root FALSE #> 24 2 Alaska 14.000000 0.000000 root TRUE #> 25 24 Mississippi 15.000000 0.000000 root TRUE #> 26 40 South Carolina 16.000000 0.000000 root TRUE #> 27 NA 15.500000 21.167192 root FALSE #> 28 NA 14.750000 28.095803 root FALSE #> 29 NA 12.187500 39.394633 root FALSE #> 30 NA 8.031250 44.283922 root FALSE #> 31 NA 4.765625 77.605024 root FALSE #> 32 47 Washington 17.000000 0.000000 root TRUE #> 33 37 Oregon 18.000000 0.000000 root TRUE #> 34 50 Wyoming 19.000000 0.000000 root TRUE #> 35 36 Oklahoma 20.000000 0.000000 root TRUE #> 36 46 Virginia 21.000000 0.000000 root TRUE #> 37 NA 20.500000 7.355270 root FALSE #> 38 NA 19.750000 10.736739 root FALSE #> 39 NA 18.875000 12.878100 root FALSE #> 40 NA 17.937500 16.425489 root FALSE #> 41 39 Rhode Island 22.000000 0.000000 root TRUE #> 42 21 Massachusetts 23.000000 0.000000 root TRUE #> 43 30 New Jersey 24.000000 0.000000 root TRUE #> 44 NA 23.500000 11.456439 root FALSE #> 45 NA 22.750000 22.595978 root FALSE #> 46 NA 20.343750 26.713777 root FALSE #> 47 25 Missouri 25.000000 0.000000 root TRUE #> 48 4 Arkansas 26.000000 0.000000 root TRUE #> 49 42 Tennessee 27.000000 0.000000 root TRUE #> 50 NA 26.500000 12.614278 root FALSE #> 51 NA 25.750000 20.198479 root FALSE #> 52 10 Georgia 28.000000 0.000000 root TRUE #> 53 6 Colorado 29.000000 0.000000 root TRUE #> 54 43 Texas 30.000000 0.000000 root TRUE #> 55 NA 29.500000 14.501034 root FALSE #> 56 NA 28.750000 23.972143 root FALSE #> 57 NA 27.250000 29.054195 root FALSE #> 58 NA 23.796875 44.837933 root FALSE #> 59 12 Idaho 31.000000 0.000000 root TRUE #> 60 27 Nebraska 32.000000 0.000000 root TRUE #> 61 17 Kentucky 33.000000 0.000000 root TRUE #> 62 26 Montana 34.000000 0.000000 root TRUE #> 63 NA 33.500000 3.834058 root FALSE #> 64 NA 32.750000 12.438692 root FALSE #> 65 NA 31.875000 15.026107 root FALSE #> 66 35 Ohio 35.000000 0.000000 root TRUE #> 67 44 Utah 36.000000 0.000000 root TRUE #> 68 NA 35.500000 6.637771 root FALSE #> 69 14 Indiana 37.000000 0.000000 root TRUE #> 70 16 Kansas 38.000000 0.000000 root TRUE #> 71 NA 37.500000 3.929377 root FALSE #> 72 7 Connecticut 39.000000 0.000000 root TRUE #> 73 38 Pennsylvania 40.000000 0.000000 root TRUE #> 74 NA 39.500000 8.027453 root FALSE #> 75 NA 38.500000 13.352260 root FALSE #> 76 NA 37.000000 15.122897 root FALSE #> 77 NA 34.437500 20.598507 root FALSE #> 78 11 Hawaii 41.000000 0.000000 root TRUE #> 79 48 West Virginia 42.000000 0.000000 root TRUE #> 80 19 Maine 43.000000 0.000000 root TRUE #> 81 41 South Dakota 44.000000 0.000000 root TRUE #> 82 NA 43.500000 8.537564 root FALSE #> 83 NA 42.750000 10.771175 root FALSE #> 84 34 North Dakota 45.000000 0.000000 root TRUE #> 85 45 Vermont 46.000000 0.000000 root TRUE #> 86 NA 45.500000 13.044922 root FALSE #> 87 23 Minnesota 47.000000 0.000000 root TRUE #> 88 49 Wisconsin 48.000000 0.000000 root TRUE #> 89 15 Iowa 49.000000 0.000000 root TRUE #> 90 29 New Hampshire 50.000000 0.000000 root TRUE #> 91 NA 49.500000 2.291288 root FALSE #> 92 NA 48.750000 10.184218 root FALSE #> 93 NA 47.875000 18.993398 root FALSE #> 94 NA 46.687500 27.779904 root FALSE #> 95 NA 44.718750 33.117815 root FALSE #> 96 NA 42.859375 41.094765 root FALSE #> 97 NA 38.648438 54.746831 root FALSE #> 98 NA 31.222656 89.232093 root FALSE "},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame","title":"Build a data frame — fortify_data_frame","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame","text":"","code":"fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame","text":"data object converted data frame. ... Arguments passed methods. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame","text":"data frame.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame.matrix","title":"Build a data frame — fortify_data_frame.matrix","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame.matrix","text":"","code":"# S3 method for class 'matrix' fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL) # S3 method for class 'DelayedMatrix' fortify_data_frame(data, ...) # S3 method for class 'Matrix' fortify_data_frame(data, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame.matrix","text":"data matrix-like object. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame.matrix","text":"Matrix transformed long-form data frame, row represents unique combination matrix indices corresponding values. resulting data frame contain following columns: .row_names .row_index: row names (applicable names exist) integer representing row index original matrix. .column_names .column_index: column names (applicable names exist) column index original matrix. value: actual value.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame.phylo","title":"Build a data frame — fortify_data_frame.phylo","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame.phylo","text":"","code":"# S3 method for class 'phylo' fortify_data_frame( data, ..., type = \"rectangle\", center = FALSE, tree_type = NULL, tip_pos = NULL, data_arg = caller_arg(data), call = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame.phylo","text":"data hclust dendrogram object. ... dots future extensions must empty. type string indicates plot type, \"rectangle\" \"triangle\". center boolean value. TRUE, nodes plotted centered respect leaves/tips branch. Otherwise (default), plot middle direct child nodes. tree_type single string, one \"phylogram\" \"cladogram\", indicating type tree. phylogram: Represents phylogenetic tree branch lengths indicate evolutionary distance time. cladogram: Represents tree branch lengths used, branches reflect evolutionary time. Usually, need modify . tip_pos x-coordinates tip. Must length number tips tree. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.phylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame.phylo","text":"data frame node coordinates: .index: original index tree tip/node. label: tip/node label text. x y: x-axis y-axis coordinates tip/node. tip: logical value indicates whether current node tip.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.phylo.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a data frame — fortify_data_frame.phylo","text":"edge: data frame edge coordinates: x y: x-axis y-axis coordinates start node edge. xend yend: x-axis y-axis coordinates terminal node edge.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.GISTIC.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a matrix from a maftools object — fortify_matrix.GISTIC","title":"Build a matrix from a maftools object — fortify_matrix.GISTIC","text":"Build matrix maftools object","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.GISTIC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a matrix from a maftools object — fortify_matrix.GISTIC","text":"","code":"# S3 method for class 'GISTIC' fortify_matrix( data, ..., n_top = NULL, bands = NULL, ignored_bands = NULL, sample_anno = NULL, remove_empty_samples = TRUE, data_arg = caller_arg(data), call = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.GISTIC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a matrix from a maftools object — fortify_matrix.GISTIC","text":"data GISTIC object. ... dots future extensions must empty. n_top single number indicates many top bands drawn. bands atomic character defines bands draw. ignored_bands atomic character defines bands ignored. sample_anno data frame sample clinical features added. remove_empty_samples single boolean value indicating whether drop samples without genomic alterations. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.GISTIC.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a matrix from a maftools object — fortify_matrix.GISTIC","text":"sample_anno: sample clinical informations provided sample_anno. sample_summary: sample copy number summary informations. See data@cnv.summary details. cytoband_summary: cytoband summary informations. See data@cytoband.summary details. gene_summary: gene summary informations. See data@gene.summary details. summary: data frame summary information. See data@summary details.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.MAF.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a matrix from a maftools object — fortify_matrix.MAF","title":"Build a matrix from a maftools object — fortify_matrix.MAF","text":"Convert MAF object matrix: fortify_matrix.MAF: Extract genomic alterations genes. fortify_matrix.MAF_pathways: Extract genomic alterations pathways. tune.MAF() helps convert MAF object MAF_pathways object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.MAF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a matrix from a maftools object — fortify_matrix.MAF","text":"","code":"# S3 method for class 'MAF' fortify_matrix( data, ..., genes = NULL, n_top = NULL, remove_empty_genes = TRUE, remove_empty_samples = TRUE, collapse_vars = TRUE, use_syn = TRUE, missing_genes = \"error\", data_arg = caller_arg(data), call = NULL ) # S3 method for class 'MAF_pathways' fortify_matrix( data, ..., pathdb = \"smgbp\", remove_empty_pathways = TRUE, remove_empty_samples = TRUE, data_arg = caller_arg(data), call = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.MAF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a matrix from a maftools object — fortify_matrix.MAF","text":"data MAF object. ... dots future extensions must empty. genes atomic character defines genes draw. n_top single number indicates many top genes drawn. remove_empty_genes single boolean value indicats whether drop genes without genomic alterations. remove_empty_samples single boolean value indicats whether drop samples without genomic alterations. collapse_vars single boolean value indicating whether collapse multiple alterations sample gene single value \"Multi_Hit\". Alternatively, can provide single string indicates collapsed values. use_syn single boolean value indicates whether include synonymous variants Classifies SNPs transitions transversions. missing_genes string, either \"error\" \"remove\", specifying action handling missing genes. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user. pathdb string \"smgbp\" \"sigpw\", named list genes define pathways. remove_empty_pathways single boolean value indicats whether drop pathways without genomic alterations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.MAF.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a matrix from a maftools object — fortify_matrix.MAF","text":"fortify_matrix.MAF: gene_summary: gene summary informations. See maftools::getGeneSummary() details. sample_summary: sample summary informations. See maftools::getSampleSummary() details. sample_anno: sample clinical informations. See maftools::getClinicalData() details. n_genes: Total genes. n_samples: Total samples. titv: list data.frames Transitions Transversions summary. See maftools::titv() details. fortify_matrix.MAF_pathways: gene_list: pathway contents. pathway_summary: pathway summary informations. See maftools::pathways() details. sample_summary: sample summary informations. See maftools::getSampleSummary() details. sample_anno: sample clinical informations. See maftools::getClinicalData() details.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.default.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a Matrix — fortify_matrix.default","title":"Build a Matrix — fortify_matrix.default","text":"default, calls .matrix() build matrix.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.default.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a Matrix — fortify_matrix.default","text":"","code":"# Default S3 method fortify_matrix(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.default.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a Matrix — fortify_matrix.default","text":"data object converted matrix. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.default.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a Matrix — fortify_matrix.default","text":"matrix.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a Matrix — fortify_matrix","title":"Build a Matrix — fortify_matrix","text":"function converts various objects matrix format. default, calls .matrix() build matrix.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a Matrix — fortify_matrix","text":"","code":"fortify_matrix(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a Matrix — fortify_matrix","text":"data object converted matrix. ... Additional arguments passed methods. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a Matrix — fortify_matrix","text":"matrix.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.list_upset.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a Matrix for UpSet plot — fortify_matrix.list_upset","title":"Build a Matrix for UpSet plot — fortify_matrix.list_upset","text":"function converts list matrix format suitable creating UpSet plot. always returns matrix horizontal UpSet plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.list_upset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a Matrix for UpSet plot — fortify_matrix.list_upset","text":"","code":"# S3 method for class 'list_upset' fortify_matrix( data, mode = \"distinct\", ..., data_arg = caller_arg(data), call = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.list_upset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a Matrix for UpSet plot — fortify_matrix.list_upset","text":"data list sets. mode string \"distinct\", \"intersect\", \"union\" indicates mode define set intersections. Check https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#upset-mode details. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.list_upset.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a Matrix for UpSet plot — fortify_matrix.list_upset","text":"intersection_sizes: integer vector indicating size intersection. set_sizes: integer vector indicating size set.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a matrix from a matrix — fortify_matrix.matrix","title":"Build a matrix from a matrix — fortify_matrix.matrix","text":"Build matrix matrix","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a matrix from a matrix — fortify_matrix.matrix","text":"","code":"# S3 method for class 'matrix' fortify_matrix(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a matrix from a matrix — fortify_matrix.matrix","text":"data matrix object. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix.html","id":"shape","dir":"Reference","previous_headings":"","what":"shape","title":"Build a matrix from a matrix — fortify_matrix.matrix","text":"upset: fortify_matrix.matrix_upset","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix_upset.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a Matrix for UpSet plot — fortify_matrix.matrix_upset","title":"Build a Matrix for UpSet plot — fortify_matrix.matrix_upset","text":"Converts matrix suitable creating UpSet plot. tune.matrix() helps convert matrix object matrix_upset object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix_upset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a Matrix for UpSet plot — fortify_matrix.matrix_upset","text":"","code":"# S3 method for class 'matrix_upset' fortify_matrix(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix_upset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a Matrix for UpSet plot — fortify_matrix.matrix_upset","text":"data matrix row represents element, column defines set. values matrix indicate whether element part set. non-missing value signifies element exists set. ... Arguments passed fortify_matrix.list_upset mode string \"distinct\", \"intersect\", \"union\" indicates mode define set intersections. Check https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#upset-mode details. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix_upset.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a Matrix for UpSet plot — fortify_matrix.matrix_upset","text":"intersection_sizes: integer vector indicating size intersection. set_sizes: integer vector indicating size set.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a matrix from phylo object — fortify_matrix.phylo","title":"Build a matrix from phylo object — fortify_matrix.phylo","text":"method allows phylo object directly input stack_discrete() circle_discrete(). makes possible add align_phylo() stack independently, align_phylo() requires layout labels.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a matrix from phylo object — fortify_matrix.phylo","text":"","code":"# S3 method for class 'phylo' fortify_matrix(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a matrix from phylo object — fortify_matrix.phylo","text":"data phylo object. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.phylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a matrix from phylo object — fortify_matrix.phylo","text":"one-column matrix tip labels values, row names also tip labels.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/free.html","id":null,"dir":"Reference","previous_headings":"","what":"Free from alignment — free_align","title":"Free from alignment — free_align","text":"align_plots try align plot panels, every elements plot, following functions romove restrictions: free_align: want compose plots without alignment panel axes (panel aligned). can wrap plot free_align. free_border: want compose plots without alignment panel borders (still align panels ), can wrap plot free_border. free_lab: want compose plots without alignment axis title, can wrap plot free_lab. free_space: Removing ggplot element sizes aligning. free_vp: Customize viewport aligning. free_guide: want override behaviour overall guides behaviour, can wrap plot free_guide.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/free.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Free from alignment — free_align","text":"","code":"free_align(plot, axes = \"tlbr\") free_border(plot, borders = \"tlbr\") free_guide(plot, guides = \"tlbr\") free_lab(plot, labs = \"tlbr\") free_space(plot, spaces = \"tlbr\") free_vp(plot, x = 0.5, y = 0.5, width = NA, height = NA, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/free.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Free from alignment — free_align","text":"plot ggplot alignpatches object. axes axes aligned? string containing one \"t\", \"l\", \"b\", \"r\". borders border aligned? string containing one \"t\", \"l\", \"b\", \"r\". guides string containing one \"t\", \"l\", \"b\", \"r\" indicates side guide legends collected plot. NULL, guide legends collected. labs axis labs free? string containing one \"t\", \"l\", \"b\", \"r\". spaces border spaces removed? string containing one \"t\", \"l\", \"b\", \"r\". x numeric vector unit object specifying x-location. y numeric vector unit object specifying y-location. width numeric vector unit object specifying width. height numeric vector unit object specifying height. ... Arguments passed grid::viewport default.units string indicating default units use x, y, width, height given numeric vectors. just string numeric vector specifying justification viewport relative (x, y) location. two values, first value specifies horizontal justification second value specifies vertical justification. Possible string values : \"left\", \"right\", \"centre\", \"center\", \"bottom\", \"top\". numeric values, 0 means left alignment 1 means right alignment. gp object class \"gpar\", typically output call function gpar. basically list graphical parameter settings. clip One \"\", \"inherit\", \"\", indicating whether clip extent viewport, inherit clipping region parent viewport, turn clipping altogether. back-compatibility, logical value TRUE corresponds \"\" FALSE corresponds \"inherit\". May also grob (gTree) describes clipping path result call .path. mask One \"none\" (FALSE) \"inherit\" (TRUE) grob (gTree) result call .mask. specifies viewport mask, inherit mask parent, mask, described grob. xscale numeric vector length two indicating minimum maximum x-scale. limits may identical. yscale numeric vector length two indicating minimum maximum y-scale. limits may identical. angle numeric value indicating angle rotation viewport. Positive values indicate amount rotation, degrees, anticlockwise positive x-axis. layout Grid layout object splits viewport subregions. layout.pos.row numeric vector giving rows occupied viewport parent's layout. layout.pos.col numeric vector giving columns occupied viewport parent's layout. name character value uniquely identify viewport pushed onto viewport tree.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/free.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Free from alignment — free_align","text":"free_align: modified version plot free_align class. free_border: modified version plot free_border class. free_guide: modified version plot free_guide class. free_lab: modified version plot free_lab class. free_space: modified version plot free_space class. free_vp: modified version plot free_vp class.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/free.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Free from alignment — free_align","text":"","code":"# directly copied from `patchwork` # Sometimes you have a plot that defies good composition alginment, e.g. due # to long axis labels p1 <- ggplot(mtcars) + geom_bar(aes(y = factor(gear), fill = factor(gear))) + scale_y_discrete( \"\", labels = c( \"3 gears are often enough\", \"But, you know, 4 is a nice number\", \"I would def go with 5 gears in a modern car\" ) ) # When combined with other plots it ends up looking bad p2 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) align_plots(p1, p2, ncol = 1L) # We can fix this be using `free_align` align_plots(free_align(p1), p2, ncol = 1L) # If we still want the panels to be aligned to the right, we can choose to # free only the left side align_plots(free_align(p1, axes = \"l\"), p2, ncol = 1L) # We could use `free_lab` to fix the layout in a different way align_plots(p1, free_lab(p2), ncol = 1L) # `free_border` is similar with `free_lab`, they have a distinction in terms # of placement on either the top or bottom side of the panel. Specifically, # the top side contains the `title` and `subtitle`, while the bottom side # contains the `caption`. free_lab() does not attach these elements in the # panel area. p3 <- ggplot(mtcars) + geom_point(aes(hp, wt, colour = mpg)) + ggtitle(\"Plot 3\") p_axis_top <- ggplot(mtcars) + geom_point(aes(mpg, disp)) + ggtitle(\"Plot axis in top\") + scale_x_continuous(position = \"top\") align_plots(p_axis_top, free_lab(p3)) align_plots(p_axis_top, free_border(p3)) # Another issue is that long labels can occupy much spaces align_plots(NULL, p1, p2, p2) # This can be fixed with `free_space` align_plots(NULL, free_space(p1, \"l\"), p2, p2)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Layer with Grid or Function — geom_draw","title":"Layer with Grid or Function — geom_draw","text":"Draw ggplot2 layer using grob function.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Layer with Grid or Function — geom_draw","text":"","code":"geom_draw( draw, mapping = NULL, data = NULL, type = \"group\", stat = \"identity\", position = \"identity\", ..., na.rm = FALSE, show.legend = FALSE, inherit.aes = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layer with Grid or Function — geom_draw","text":"draw Either grob object function (can purrr-style) accepts least three arguments (data, panel_params coord) returns grob. draw function, used draw_group/draw_panel function Geom ggproto object. always call coord$transform(data, panel_params) inside function draw obtain transformed data plot scales. mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). type single string \"group\" \"panel\", \"group\" draws geoms draw_group, displays multiple observations one geometric object, \"panel\" draws geoms draw_panel, displaying individual graphical objects observation (row). Default: \"group\". stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend. na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Layer with Grid or Function — geom_draw","text":"want combine functionality multiple geoms, can typically achieved preparing data geom inside draw_*() call sending different geoms, collecting output grid::gList (list grobs) draw_group() grid::gTree (grob containing multiple child grobs) draw_panel().","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layer with Grid or Function — geom_draw","text":"","code":"text <- grid::textGrob( \"ggdraw\", x = c(0, 0, 0.5, 1, 1), y = c(0, 1, 0.5, 0, 1), hjust = c(0, 0, 0.5, 1, 1), vjust = c(0, 1, 0.5, 0, 1) ) ggplot(data.frame(x = 1, y = 2)) + geom_draw(text)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":null,"dir":"Reference","previous_headings":"","what":"Layer with customized draw function — geom_draw2","title":"Layer with customized draw function — geom_draw2","text":"Layer customized draw function","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Layer with customized draw function — geom_draw2","text":"","code":"geom_draw2( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., na.rm = FALSE, show.legend = NA, inherit.aes = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layer with customized draw function — geom_draw2","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. ... Additional arguments passed draw aesthetic. na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Layer with customized draw function — geom_draw2","text":"geom_draw2 depends new aesthetics draw, always provided scale_draw_manual(), , can provide list functions define value drawn. ggplot2 aesthetics can used arguments.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Layer with customized draw function — geom_draw2","text":"geom_draw2() understands following aesthetics (required aesthetics bold): draw alpha colour fill group linetype linewidth shape size stroke x y Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\").","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layer with customized draw function — geom_draw2","text":"","code":"library(grid) ggplot(data.frame(value = letters[seq_len(5)], y = seq_len(5))) + geom_draw2(aes(x = 1, y = y, draw = value, fill = value)) + scale_draw_manual(values = list( a = function(x, y, width, height, fill) { rectGrob(x, y, width = width, height = height, gp = gpar(fill = fill), default.units = \"native\" ) }, b = function(x, y, width, height, fill) { rectGrob(x, y, width = width, height = height, gp = gpar(fill = fill), default.units = \"native\" ) }, c = function(x, y, width, height, fill) { rectGrob(x, y, width = width, height = height, gp = gpar(fill = fill), default.units = \"native\" ) }, d = function(x, y, width, height, shape) { gList( pointsGrob(x, y, pch = shape), # To ensure the rectangle color is shown in the legends, you # must explicitly provide a color argument and include it in # the `gpar()` of the graphical object rectGrob(x, y, width, height, gp = gpar(col = \"black\", fill = NA) ) ) }, e = function(xmin, xmax, ymin, ymax) { segmentsGrob( xmin, ymin, xmax, ymax, gp = gpar(lwd = 2) ) } )) + scale_fill_brewer(palette = \"Dark2\") + theme_void()"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":null,"dir":"Reference","previous_headings":"","what":"Pie charts — geom_pie","title":"Pie charts — geom_pie","text":"Pie charts","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pie charts — geom_pie","text":"","code":"geom_pie( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., clockwise = TRUE, steps = 100, lineend = \"butt\", linejoin = \"round\", linemitre = 10, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pie charts — geom_pie","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend. clockwise single boolean value indicates clockwise . steps integer indicating number steps generate pie chart radian. Increasing value results smoother pie circular. lineend Line end style (round, butt, square). linejoin Line join style (round, mitre, bevel). linemitre Line mitre limit (number greater 1). na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":"new-aesthetics","dir":"Reference","previous_headings":"","what":"new aesthetics","title":"Pie charts — geom_pie","text":"angle: pie circle angle. angle0: initial pie circle angle. radius: circle radius.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Pie charts — geom_pie","text":"geom_pie() understands following aesthetics (required aesthetics bold): x y angle alpha angle0 colour fill group linetype linewidth radius Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\").","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pie charts — geom_pie","text":"","code":"ggplot(data.frame(x = 1:10, y = 1:10, value = 1:10 / sum(1:10))) + geom_pie(aes(x, y, angle = value * 360))"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_rect3d.html","id":null,"dir":"Reference","previous_headings":"","what":"Add z-aesthetic for geom_tile — geom_rect3d","title":"Add z-aesthetic for geom_tile — geom_rect3d","text":"Add z-aesthetic geom_tile","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_rect3d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add z-aesthetic for geom_tile — geom_rect3d","text":"","code":"geom_rect3d( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., lineend = \"butt\", linejoin = \"round\", linemitre = 10, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE ) geom_tile3d( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., lineend = \"butt\", linejoin = \"round\", linemitre = 10, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_rect3d.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add z-aesthetic for geom_tile — geom_rect3d","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend. lineend Line end style (round, butt, square). linejoin Line join style (round, mitre, bevel). linemitre Line mitre limit (number greater 1). na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_rect3d.html","id":"new-aesthetics","dir":"Reference","previous_headings":"","what":"new aesthetics","title":"Add z-aesthetic for geom_tile — geom_rect3d","text":"z: third dimention (z direction). theta: Angle x-axis z-axis.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_rect3d.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Add z-aesthetic for geom_tile — geom_rect3d","text":"geom_rect3d() understands following aesthetics (required aesthetics bold): xmin xmax ymin ymax z alpha colour fill group linetype linewidth Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\"). geom_tile3d() understands following aesthetics (required aesthetics bold): x y z alpha colour fill group height linetype linewidth width Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\").","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_subrect.html","id":null,"dir":"Reference","previous_headings":"","what":"Subdivide Rectangles — geom_subrect","title":"Subdivide Rectangles — geom_subrect","text":"geoms subdivide rectangles shared borders grid. geoms achieve result differ rectangles parameterized: geom_subrect(): Defines rectangles using four corners (xmin, xmax, ymin, ymax). geom_subtile(): Defines rectangles using center (x, y) dimensions (width, height).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_subrect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subdivide Rectangles — geom_subrect","text":"","code":"geom_subrect( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., byrow = TRUE, direction = NULL, lineend = \"butt\", linejoin = \"mitre\", na.rm = FALSE, show.legend = NA, inherit.aes = TRUE ) geom_subtile( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., byrow = TRUE, direction = NULL, lineend = \"butt\", linejoin = \"mitre\", na.rm = FALSE, show.legend = NA, inherit.aes = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_subrect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subdivide Rectangles — geom_subrect","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend. byrow single boolean value indicates whether arrange divided rectangles row-major order. direction string specifying arrangement direction: \"h\"(horizontal): Creates single row (one-row layout). \"v\"(vertical): Creates single column (one-column layout). NULL: Automatically determines layout dimensions using logic similar facet_wrap(). lineend Line end style (round, butt, square). linejoin Line join style (round, mitre, bevel). na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_subrect.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Subdivide Rectangles — geom_subrect","text":"geom_subrect() understands following aesthetics (required aesthetics bold): xmin xmax ymin ymax alpha colour fill group linetype linewidth Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\"). geom_subtile() understands following aesthetics (required aesthetics bold): x y alpha colour fill group height linetype linewidth width Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\").","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_subrect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subdivide Rectangles — geom_subrect","text":"","code":"# arranges by row ggplot(data.frame(value = letters[seq_len(5)])) + geom_subtile(aes(x = 1, y = 1, fill = value)) #> `geom_subtile()` subdivide tile into a maximal of 5 rectangles # arranges by column ggplot(data.frame(value = letters[seq_len(9)])) + geom_subtile(aes(x = 1, y = 1, fill = value), byrow = FALSE) #> `geom_subtile()` subdivide tile into a maximal of 9 rectangles # one-row ggplot(data.frame(value = letters[seq_len(4)])) + geom_subtile(aes(x = 1, y = 1, fill = value), direction = \"h\") #> `geom_subtile()` subdivide tile into a maximal of 4 rectangles # one-column ggplot(data.frame(value = letters[seq_len(4)])) + geom_subtile(aes(x = 1, y = 1, fill = value), direction = \"v\") #> `geom_subtile()` subdivide tile into a maximal of 4 rectangles"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign-package.html","id":null,"dir":"Reference","previous_headings":"","what":"ggalign: A 'ggplot2' Extension for Consistent Axis Alignment — ggalign-package","title":"ggalign: A 'ggplot2' Extension for Consistent Axis Alignment — ggalign-package","text":"'ggplot2' extension offers various tools organizing arranging plots. designed consistently align specific axis across multiple 'ggplot' objects, making especially useful plots requiring data order manipulation. typical use case includes organizing combinations like dendrogram heatmap.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"ggalign: A 'ggplot2' Extension for Consistent Axis Alignment — ggalign-package","text":"Maintainer: Yun Peng yunyunp96@163.com (ORCID) Authors: Shixiang Wang w_shixiang@163.com (ORCID)","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":null,"dir":"Reference","previous_headings":"","what":"Add ggplot by Aligning discrete or continuous variable — ggalign","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"ggalign() similar ggplot initializes ggplot data mapping. ggalign() allowing provide data various formats, including matrices, data frames, simple vectors. default, inherit layout. function, apply layout matrix. ggalign() focuses integrating plots layout aligning axes.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"","code":"ggalign( data = waiver(), mapping = aes(), ..., size = NULL, no_axes = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"data following options can used: NULL: data set. waiver(): Inherits data layout matrix. function (including purrr-like lambda syntax): Applied layout matrix transform data use. transform final plot data, please use scheme_data(). matrix, data.frame, atomic vector. mapping Default list aesthetic mappings use plot. specified, must supplied layer added plot. ... Additional arguments passed fortify_data_frame(). size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. no_axes Logical; TRUE, removes axes elements alignment axis using theme_no_axes(). default, use option- \"ggalign.align_no_axes\". active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"ggalign initializes ggplot object. underlying data created using fortify_data_frame(). Please refer details. aligning discrete variables, ggalign() always applies default mapping axis data index layout. Specifically: aes(y = .data$.y) used horizontal stack_layout() (including left right annotations). aes(x = .data$.x) used vertical stack_layout() (including top bottom annotations) circle_layout(). following columns added data frame align discrete variables: .panel: panel aligned axis. Refers x-axis vertical stack_layout() (including top bottom annotations), y-axis horizontal stack_layout() (including left right annotations). .names (vec_names()) .index (vec_size()/NROW()): Character names (available) integer index original data. .x/.y .discrete_x/.discrete_y: Integer indices x/y coordinates, factor data labels (applicable names exist). recommended use .x/.y, .discrete_x/.discrete_y x/y mapping. data inherits quad_layout()/ggheatmap(), additional columns added: .extra_panel: Provides panel information column (left right annotation) row (top bottom annotation). .extra_index: index information column (left right annotation) row (top bottom annotation).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"","code":"ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + ggalign() + geom_point(aes(y = value)) #> → heatmap built with `geom_tile()` ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top(size = 0.5) + align_dendro(k = 3L) + ggalign(data = NULL, size = 0.2) + geom_tile(aes(y = 1L, fill = .panel)) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalignGrob.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a plot grob. — ggalignGrob","title":"Generate a plot grob. — ggalignGrob","text":"Generate plot grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalignGrob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a plot grob. — ggalignGrob","text":"","code":"ggalignGrob(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalignGrob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a plot grob. — ggalignGrob","text":"x object converted grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalignGrob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a plot grob. — ggalignGrob","text":"grob() object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalignGrob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a plot grob. — ggalignGrob","text":"","code":"ggalignGrob(ggplot()) #> TableGrob (20 x 17) \"layout\": 26 grobs #> z cells name grob #> 1 0 ( 1-20, 1-17) background rect[plot.background..rect.3459] #> 2 5 ( 9- 9, 7- 7) spacer zeroGrob[NULL] #> 3 7 (11-11, 7- 7) axis-l zeroGrob[NULL] #> 4 3 (13-13, 7- 7) spacer zeroGrob[NULL] #> 5 6 ( 9- 9, 9- 9) axis-t zeroGrob[NULL] #> 6 1 (11-11, 9- 9) panel gTree[panel-1.gTree.3454] #> 7 9 (13-13, 9- 9) axis-b zeroGrob[NULL] #> 8 4 ( 9- 9,11-11) spacer zeroGrob[NULL] #> 9 8 (11-11,11-11) axis-r zeroGrob[NULL] #> 10 2 (13-13,11-11) spacer zeroGrob[NULL] #> 11 10 ( 8- 8, 9- 9) xlab-t zeroGrob[NULL] #> 12 11 (14-14, 9- 9) xlab-b zeroGrob[NULL] #> 13 12 (11-11, 6- 6) ylab-l zeroGrob[NULL] #> 14 13 (11-11,12-12) ylab-r zeroGrob[NULL] #> 15 14 (11-11,15-15) guide-box-right zeroGrob[NULL] #> 16 15 (11-11, 3- 3) guide-box-left zeroGrob[NULL] #> 17 16 (17-17, 9- 9) guide-box-bottom zeroGrob[NULL] #> 18 17 ( 5- 5, 9- 9) guide-box-top zeroGrob[NULL] #> 19 18 (11-11, 9- 9) guide-box-inside zeroGrob[NULL] #> 20 19 ( 4- 4, 9- 9) subtitle zeroGrob[plot.subtitle..zeroGrob.3456] #> 21 20 ( 3- 3, 9- 9) title zeroGrob[plot.title..zeroGrob.3455] #> 22 21 (18-18, 9- 9) caption zeroGrob[plot.caption..zeroGrob.3457] #> 23 22 ( 7- 7, 9- 9) patch-title-top zeroGrob[NULL] #> 24 23 (11-11, 5- 5) patch-title-left zeroGrob[NULL] #> 25 24 (15-15, 9- 9) patch-title-bottom zeroGrob[NULL] #> 26 25 (11-11,13-13) patch-title-right zeroGrob[NULL]"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Data from the Attribute Attached by ggalign — ggalign_attr","title":"Get Data from the Attribute Attached by ggalign — ggalign_attr","text":"ggalign_attr provides access supplementary information stored attributes layout rendering process. attributes, commonly attached data transformation functions like fortify_matrix() fortify_data_frame(), can include essential details filtered supplementary data inform downstream operations. additional attribute, stores factor levels, can accessed ggalign_lvls.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Data from the Attribute Attached by ggalign — ggalign_attr","text":"","code":"ggalign_attr(x, field = NULL, check = TRUE) ggalign_lvls(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Data from the Attribute Attached by ggalign — ggalign_attr","text":"x Data used, typically inherited layout quad_layout()/ggheatmap() stack_layout() object. field string specifying particular data retrieve attached attribute. NULL, entire attached attribute list returned. check boolean indicating whether check field exists. TRUE, error raised specified field exist.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Data from the Attribute Attached by ggalign — ggalign_attr","text":"ggalign_attr: specified data attached supplementary data NULL unavailable. ggalign_lvls: attached supplementary levels NULL unavailable.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_attr.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Data from the Attribute Attached by ggalign — ggalign_attr","text":"Attributes attached data especially useful input data transformed ways limit access complete dataset. example, fortify_matrix.MAF() might filter mutation data adding attributes retain important context, total number observations, detailed aggregated analyses. Additionally, stores levels Variant_Classification usage.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_data_set.html","id":null,"dir":"Reference","previous_headings":"","what":"Attach supplementary data and levels for ggalign — ggalign_data_set","title":"Attach supplementary data and levels for ggalign — ggalign_data_set","text":"Attach supplementary data levels ggalign","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_data_set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Attach supplementary data and levels for ggalign — ggalign_data_set","text":"","code":"ggalign_data_set(.data, ..., .lvls = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_data_set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Attach supplementary data and levels for ggalign — ggalign_data_set","text":".data Input data layout. ... list data attached. .lvls character vector representing attached levels.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_data_set.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Attach supplementary data and levels for ggalign — ggalign_data_set","text":"Used developers fortify_matrix(), fortify_data_frame(), related methods.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_stat.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the statistics from the layout — ggalign_stat","title":"Get the statistics from the layout — ggalign_stat","text":"Get statistics layout","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_stat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the statistics from the layout — ggalign_stat","text":"","code":"ggalign_stat(x, ...) # S3 method for class 'QuadLayout' ggalign_stat(x, position, ...) # S3 method for class 'StackLayout' ggalign_stat(x, what, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_stat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the statistics from the layout — ggalign_stat","text":"x quad_layout()/ggheatmap() stack_layout() object. ... Arguments passed methods. position string \"top\", \"left\", \"bottom\", \"right\". single number string plot elements stack layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_stat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the statistics from the layout — ggalign_stat","text":"statistics","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggcross.html","id":null,"dir":"Reference","previous_headings":"","what":"Connect two layout crosswise — ggcross","title":"Connect two layout crosswise — ggcross","text":"ggcross resets layout ordering index stack_cross(). allows add align_* objects define new layout ordering index. objects added ggcross use updated layout ordering index. feature particularly useful creating tanglegram visualizations. ggcross() alias ggcross().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggcross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Connect two layout crosswise — ggcross","text":"","code":"ggcross(mapping = aes(), size = NULL, no_axes = NULL, active = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggcross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Connect two layout crosswise — ggcross","text":"mapping Default list aesthetic mappings use plot. specified, must supplied layer added plot. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. no_axes Logical; TRUE, removes axes elements alignment axis using theme_no_axes(). default, use option- \"ggalign.align_no_axes\". active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggcross.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Connect two layout crosswise — ggcross","text":"ggcross() initializes ggplot data mapping. ggcross() always applies default mapping axis data index layout. mapping aes(y = .data$.y) horizontal stack layout (including left right annotation) aes(x = .data$.x) vertical stack layout (including top bottom annotation). data underlying ggplot object contain following columns: .panel: panel aligned axis. Refers x-axis vertical stack_layout() (including top bottom annotations), y-axis horizontal stack_layout() (including left right annotations). .names (vec_names()) .index (vec_size()/NROW()): Character names (available) integer index original data. .hand: factor indicates index groups. .x/.y .discrete_x/.discrete_y: Integer indices x/y coordinates, factor data labels (applicable names exist). recommended use .x/.y, .discrete_x/.discrete_y x/y mapping.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggfree.html","id":null,"dir":"Reference","previous_headings":"","what":"Add ggplot to layout without alignment — ggfree","title":"Add ggplot to layout without alignment — ggfree","text":"ggfree() function allows incorporate ggplot object layout. Unlike ggalign(), aligns every axis value precisely, ggfree() focuses integrating plots layout without enforcing strict axis alignment.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggfree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add ggplot to layout without alignment — ggfree","text":"","code":"ggfree(data = waiver(), ..., size = NULL, active = NULL) # Default S3 method ggfree(data = waiver(), mapping = aes(), ..., size = NULL, active = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggfree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add ggplot to layout without alignment — ggfree","text":"data following options can used: NULL: data set. waiver(): Inherits data layout matrix. function (including purrr-like lambda syntax): Applied layout matrix transform data use. transform final plot data, please use scheme_data(). matrix, data.frame, atomic vector. ... Additional arguments passed fortify_data_frame(). size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. active active() object defines context settings added layout. mapping Default list aesthetic mappings use plot. specified, must supplied layer added plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggfree.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Add ggplot to layout without alignment — ggfree","text":"ggalign initializes ggplot object. underlying data created using fortify_data_frame(). Please refer method details. used quad_layout()/ggheatmap(), data inherited quad_layout() direction aligns discrete variables, following columns added: .extra_panel: Provides panel information column (left right annotation) row (top bottom annotation). .extra_index: index information column (left right annotation) row (top bottom annotation).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggfree.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add ggplot to layout without alignment — ggfree","text":"","code":"ggheatmap(matrix(rnorm(56), nrow = 7)) + anno_top() + align_dendro() + ggfree(mtcars, aes(wt, mpg)) + geom_point() #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggmark.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a plot to annotate selected observations — ggmark","title":"Add a plot to annotate selected observations — ggmark","text":"Add plot annotate selected observations","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggmark.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a plot to annotate selected observations — ggmark","text":"","code":"ggmark( mark, data = waiver(), mapping = aes(), ..., group1 = NULL, group2 = NULL, obs_size = 1, size = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggmark.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a plot to annotate selected observations — ggmark","text":"mark mark_draw() object define draw links. Like mark_line(), mark_tetragon(). Note names pair links used define panel names must unique. data following options can used: NULL: data set. waiver(): Inherits data layout matrix. function (including purrr-like lambda syntax): Applied layout matrix transform data use. transform final plot data, please use scheme_data(). matrix, data.frame, atomic vector. mapping Default list aesthetic mappings use plot. specified, must supplied layer added plot. ... Additional arguments passed fortify_data_frame(). group1, group2 single boolean value indicating whether use panel group information layout paired groups. default, specific observations selected mark, ggmark() automatically connect observations group according layout's defined groups. obs_size single numeric value indicates size single observation, ranging (0, 1]. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggmark.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Add a plot to annotate selected observations — ggmark","text":"ggmark initializes ggplot object. underlying data created using fortify_data_frame(). Please refer details. addition, following columns added data frame: .panel: panel aligned axis. means x-axis vertical stack layout (including top bottom annotation), y-axis horizontal stack layout (including left right annotation). .names (vec_names()) .index (vec_size()/NROW()): character names (applicable names exists) integer index original data. .hand: factor levels c(\"left\", \"right\") horizontal stack layouts, c(\"top\", \"bottom\") vertical stack layouts, indicating position linked observations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggmark.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a plot to annotate selected observations — ggmark","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) rownames(small_mat) <- paste0(\"row\", seq_len(nrow(small_mat))) colnames(small_mat) <- paste0(\"column\", seq_len(ncol(small_mat))) # mark_line ggheatmap(small_mat) + theme(axis.text.x = element_text(hjust = 0, angle = -60)) + anno_right() + align_kmeans(3L) + ggmark(mark_line(I(1:3) ~ NULL)) + geom_boxplot(aes(.names, value)) + theme(plot.margin = margin(l = 0.1, t = 0.1, unit = \"npc\")) #> → heatmap built with `geom_tile()` # mark_tetragon ggheatmap(small_mat) + theme(axis.text.x = element_text(hjust = 0, angle = -60)) + anno_right() + align_kmeans(3L) + ggmark(mark_tetragon(I(1:3) ~ NULL)) + geom_boxplot(aes(.names, value)) + theme(plot.margin = margin(l = 0.1, t = 0.1, unit = \"npc\")) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an OncoPrint — ggoncoplot","title":"Create an OncoPrint — ggoncoplot","text":"ggoncoplot() function generates oncoPrint visualizations display genetic alterations matrix format. function especially useful visualizing complex genomic data, mutations, copy number variations, genomic alterations cancer research.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an OncoPrint — ggoncoplot","text":"","code":"ggoncoplot( data = NULL, mapping = aes(), ..., map_width = NULL, map_height = NULL, reorder_row = reorder_column, reorder_column = TRUE, width = NA, height = NA, filling = waiver(), theme = NULL, active = NULL ) # Default S3 method ggoncoplot( data = NULL, mapping = aes(), ..., map_width = NULL, map_height = NULL, reorder_row = reorder_column, reorder_column = TRUE, width = NA, height = NA, filling = waiver(), theme = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an OncoPrint — ggoncoplot","text":"data character matrix encodes alterations, can use \";\", \":\", \",\", \"|\" separate multiple alterations. mapping Default list aesthetic mappings use main plot layout. specified, must supplied layer added main plot. ... Additional arguments passed fortify_matrix(). map_width, map_height named numeric value defines width/height alterations. reorder_row boolean value indicating whether reorder rows based frequency alterations. can set FALSE, add align_order(~rowSums(!.na(.x)), reverse = TRUE) achieve result. may also need set strit = FALSE align_order() already groups. reorder_column boolean value indicating whether reorder columns based characteristics alterations. can set FALSE, add align_reorder(memo_order) achieve result. may also need set strit = FALSE align_reorder() already groups. width, height relative width/height main plot, can unit object. filling ggheatmap(), \"tile\" can used. theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an OncoPrint — ggoncoplot","text":"HeatmapLayout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create an OncoPrint — ggoncoplot","text":"ggoncoplot() wrapper around ggheatmap() function, designed simplify creation OncoPrint-style visualizations. function automatically processes input character matrix splitting encoded alterations (delimited \";\", \":\", \",\", \"|\") individual genomic events unnesting columns visualization.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an OncoPrint — ggoncoplot","text":"","code":"# A simple example from `ComplexHeatmap` mat <- read.table(textConnection( \"s1,s2,s3 g1,snv;indel,snv,indel g2,,snv;indel,snv g3,snv,,indel;snv\" ), row.names = 1, header = TRUE, sep = \",\", stringsAsFactors = FALSE) ggoncoplot(mat, map_width = c(snv = 0.5), map_height = c(indel = 0.9)) + # Note that guide legends from `geom_tile` and `geom_bar` are different. # Although they appear similar, the internal mechanisms won't collapse # the guide legends. Therefore, we remove the guide legends from # `geom_tile`. guides(fill = \"none\") + anno_top(size = 0.5) + ggalign() + geom_bar(aes(fill = value), data = function(x) { subset(x, !is.na(value)) }) + anno_right(size = 0.5) + ggalign() + geom_bar(aes(fill = value), orientation = \"y\", data = function(x) { subset(x, !is.na(value)) }) & scale_fill_brewer(palette = \"Dark2\", na.translate = FALSE)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggupset.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an UpSet plot — ggupset","title":"Create an UpSet plot — ggupset","text":"ggupset specialized version quad_discrete(), simplifies creation Upset plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggupset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an UpSet plot — ggupset","text":"","code":"ggupset( data = NULL, mapping = aes(), ..., direction = \"h\", point = NULL, line = NULL, rect = NULL, width = NA, height = NA, theme = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggupset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an UpSet plot — ggupset","text":"data Data used create UpSet plot. fortify_matrix() used convert data matrix. Currently, fortify_matrix.list_upset fortify_matrix.matrix_upset suitable creating UpSet plot. mapping Default list aesthetic mappings use main plot layout. specified, must supplied layer added main plot. ... Additional arguments passed fortify_matrix(). direction string indicating direction UpSet plot, \"h\"(horizontal) \"v\"(vertical). vertical UpSet plot, columns matrix correspond sets, rows correspond intersections. default, horizontal UpSet plot used, rows matrix correspond sets columns correspond intersections. point list parameters passed geom_point(). line list parameters passed geom_line(). rect list parameters passed geom_rect(). width, height relative width/height main plot, can unit object. theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggupset.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Create an UpSet plot — ggupset","text":"data input converted matrix using fortify_matrix(), data underlying main plot contain following columns: .panel_x .panel_y: column row panel groups. .x .y: integer index x y coordinates .discrete_x .discrete_y: factor data labels (applicable .row_names .column_names exists). .row_names .column_names: character row column names original matrix (applicable names exist). .row_index .column_index: row column index original matrix. value: actual matrix value.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggupset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an UpSet plot — ggupset","text":"","code":"set.seed(123) lt <- list( a = sample(letters, 5), b = sample(letters, 10), c = sample(letters, 15) ) ggupset(tune(lt)) + scale_fill_manual(values = c(\"#F0F0F0\", \"white\"), guide = \"none\") + scale_color_manual(values = c(\"grey\", \"black\"), guide = \"none\") + anno_top() + ggalign(data = function(d) ggalign_attr(d, \"intersection_sizes\")) + ggplot2::geom_bar(aes(y = .data$value), stat = \"identity\") + anno_right() + ggalign(data = function(d) ggalign_attr(d, \"set_sizes\")) + ggplot2::geom_bar(aes(x = .data$value), stat = \"identity\", orientation = \"y\" )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggwrap.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrap Arbitrary Graphics to ggplot — ggwrap","title":"Wrap Arbitrary Graphics to ggplot — ggwrap","text":"ggwrap() function allows non-ggplot2 elements converted compliant representation use align_plots(). useful adding graphics can converted grob patch() method.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggwrap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrap Arbitrary Graphics to ggplot — ggwrap","text":"","code":"ggwrap(plot, ..., align = \"panel\", on_top = FALSE, clip = TRUE, vp = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggwrap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrap Arbitrary Graphics to ggplot — ggwrap","text":"plot graphic can converted grob using patch(). ... Additional arguments passed patch() method. align string specifying area place plot: \"full\" full area, \"plot\" full plotting area (including axis label), \"panel\" actual area data drawn. on_top single boolean value indicates whether graphic plot put frontmost. Note: graphic plot always put background. clip single boolean value indicating whether grob clipped expand outside designated area. vp viewport object, can use define plot area.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggwrap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrap Arbitrary Graphics to ggplot — ggwrap","text":"wrapped_plot object can directly placed align_plots().","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggwrap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrap Arbitrary Graphics to ggplot — ggwrap","text":"","code":"library(grid) ggwrap(rectGrob(gp = gpar(fill = \"goldenrod\")), align = \"full\") + inset(rectGrob(gp = gpar(fill = \"steelblue\")), align = \"panel\") + inset(textGrob(\"Here are some text\", gp = gpar(color = \"black\")), align = \"panel\" ) p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) + ggtitle(\"Plot 1\") align_plots(p1, ggwrap( ~ plot(mtcars$mpg, mtcars$disp), mar = c(0, 2, 0, 0), bg = NA ))"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/hclust2.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate Tree Structures with Hierarchical Clustering — hclust2","title":"Generate Tree Structures with Hierarchical Clustering — hclust2","text":"Generate Tree Structures Hierarchical Clustering","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/hclust2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate Tree Structures with Hierarchical Clustering — hclust2","text":"","code":"hclust2( matrix, distance = \"euclidean\", method = \"complete\", use_missing = \"pairwise.complete.obs\" )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/hclust2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate Tree Structures with Hierarchical Clustering — hclust2","text":"matrix numeric matrix, data frame. distance string distance measure used. must one \"euclidean\", \"maximum\", \"manhattan\", \"canberra\", \"binary\" \"minkowski\". Correlation coefficient can also used, including \"pearson\", \"spearman\" \"kendall\". way, 1 - cor used distance. addition, can also provide dist object directly function return dist object. Use NULL, want calculate distance. method string agglomeration method used. (unambiguous abbreviation ) one \"ward.D\", \"ward.D2\", \"single\", \"complete\", \"average\" (= UPGMA), \"mcquitty\" (= WPGMA), \"median\" (= WPGMC) \"centroid\" (= UPGMC). can also provide function accepts calculated distance (input matrix distance NULL) returns hclust object. Alternative, can supply object can coerced hclust. use_missing optional character string giving method computing covariances presence missing values. must (abbreviation ) one strings \"everything\", \".obs\", \"complete.obs\", \"na..complete\", \"pairwise.complete.obs\". used distance correlation coefficient string.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/hclust2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate Tree Structures with Hierarchical Clustering — hclust2","text":"hclust object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/hclust2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate Tree Structures with Hierarchical Clustering — hclust2","text":"","code":"hclust2(dist(USArrests), method = \"ward.D\") #> #> Call: #> stats::hclust(d = d, method = method) #> #> Cluster method : ward.D #> Distance : euclidean #> Number of objects: 50 #>"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a heatmap — heatmap_layout","title":"Create a heatmap — heatmap_layout","text":"heatmap_layout specialized version quad_discrete(), simplifies creation heatmap plots integrating essential elements standard heatmap layout, ensuring appropriate data mapping visualization layers automatically applied. ggheatmap alias heatmap_layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a heatmap — heatmap_layout","text":"","code":"heatmap_layout( data = NULL, mapping = aes(), ..., width = NA, height = NA, filling = waiver(), theme = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a heatmap — heatmap_layout","text":"data Default dataset use layout. specified, must supplied plot added layout. default, try inherit parent layout. fortify_matrix() used convert data matrix. mapping Default list aesthetic mappings use main plot layout. specified, must supplied layer added main plot. ... Additional arguments passed fortify_matrix(). width, height relative width/height main plot, can unit object. filling single string \"raster\" \"tile\" indicate filling style. default, waiver() used, means input matrix 20,000 cells (nrow * ncol > 20000), geom_raster() used performance efficiency; smaller matrices, geom_tile() used. customize filling style, set NULL. backward compatibility, single boolean value acceptable: TRUE means waiver(), FALSE means NULL. default, classic heatmap color scheme scale_fill_gradient2(low = \"blue\", high = \"red\") utilized continuous values. can use options \"ggalign.heatmap_continuous_fill\" \"ggalign.heatmap_discrete_fill\" modify default heatmap body filling color scale. See scale_fill_continuous() scale_fill_discrete() details option settings. theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a heatmap — heatmap_layout","text":"HeatmapLayout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Create a heatmap — heatmap_layout","text":"data input converted matrix using fortify_matrix(), data underlying main plot contain following columns: .panel_x .panel_y: column row panel groups. .x .y: integer index x y coordinates .discrete_x .discrete_y: factor data labels (applicable .row_names .column_names exists). .row_names .column_names: character row column names original matrix (applicable names exist). .row_index .column_index: row column index original matrix. value: actual matrix value.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a heatmap — heatmap_layout","text":"","code":"ggheatmap(1:10) #> → heatmap built with `geom_tile()` ggheatmap(letters) #> → heatmap built with `geom_tile()` ggheatmap(matrix(rnorm(81), nrow = 9L)) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/inset.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a ggplot inset — inset","title":"Create a ggplot inset — inset","text":"Create ggplot inset","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/inset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a ggplot inset — inset","text":"","code":"inset(plot, ..., align = \"panel\", on_top = TRUE, clip = TRUE, vp = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/inset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a ggplot inset — inset","text":"plot graphic can converted grob using patch(). ... Additional arguments passed patch() method. align string specifying area place plot: \"full\" full area, \"plot\" full plotting area (including axis label), \"panel\" actual area data drawn. on_top single boolean value indicates whether graphic plot put frontmost. Note: graphic plot always put background. clip single boolean value indicating whether grob clipped expand outside designated area. vp viewport object, can use define plot area.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/inset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a ggplot inset — inset","text":"patch_inset object, can added ggplot.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/inset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a ggplot inset — inset","text":"","code":"library(grid) p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p1 + inset(p2, vp = viewport(0.6, 0.6, just = c(0, 0), width = 0.4, height = 0.4 ))"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/is_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Reports whether x is layout object — is_layout","title":"Reports whether x is layout object — is_layout","text":"Reports whether x layout object","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/is_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reports whether x is layout object — is_layout","text":"","code":"is_layout(x) is_quad_layout(x) is_stack_layout(x) is_stack_cross(x) is_circle_layout(x) is_heatmap_layout(x) is_ggheatmap(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/is_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reports whether x is layout object — is_layout","text":"x object test.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/is_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reports whether x is layout object — is_layout","text":"single boolean value.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/is_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reports whether x is layout object — is_layout","text":"","code":"is_layout(ggheatmap(1:10)) #> [1] TRUE # for quad_layout() is_quad_layout(quad_alignb(1:10)) #> [1] TRUE is_quad_layout(quad_alignh(1:10)) #> [1] TRUE is_quad_layout(quad_alignv(1:10)) #> [1] TRUE is_quad_layout(quad_free(mtcars)) #> [1] TRUE # for stack_layout() is_stack_layout(stack_discrete(\"h\", 1:10)) #> [1] TRUE is_stack_layout(stack_continuous(\"h\", 1:10)) #> [1] TRUE # for heatmap_layout() is_heatmap_layout(ggheatmap(1:10)) #> [1] TRUE is_ggheatmap(ggheatmap(1:10)) #> [1] TRUE"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layer_order.html","id":null,"dir":"Reference","previous_headings":"","what":"Change the layer adding order — layer_order","title":"Change the layer adding order — layer_order","text":"function allows change order layers added ggplot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layer_order.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change the layer adding order — layer_order","text":"","code":"layer_order(layer, order = 0)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layer_order.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change the layer adding order — layer_order","text":"layer layer geometry object added. order integer indicating position layer added. <= 0, layer added beginning. greater number plot layers, added end.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layer_order.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change the layer adding order — layer_order","text":"layer_order object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layer_order.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Change the layer adding order — layer_order","text":"","code":"ggplot(faithfuld, aes(waiting, eruptions)) + geom_raster(aes(fill = density)) + geom_point(color = \"red\", size = 1) ggplot(faithfuld, aes(waiting, eruptions)) + geom_raster(aes(fill = density)) + layer_order(geom_point(color = \"red\", size = 1))"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout-operator.html","id":null,"dir":"Reference","previous_headings":"","what":"Layout operator — layout-operator","title":"Layout operator — layout-operator","text":"+: Adds elements active plot active layout. &: Applies elements plots layout. -: Adds elements multiple plots layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout-operator.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layout operator — layout-operator","text":"e1 quad_layout()/ggheatmap() stack_layout() object. e2 object added plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout-operator.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Layout operator — layout-operator","text":"modified Layout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout-operator.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Layout operator — layout-operator","text":"+ operator straightforward used needed. order reduce code repetition ggalign provides two operators adding ggplot elements (geoms, themes, facets, etc.) multiple/plots quad_layout()/ggheatmap() stack_layout() object: - &.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout-operator.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layout operator — layout-operator","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) ggheatmap(small_mat) + anno_top() + ggalign() + geom_point(aes(y = value)) #> → heatmap built with `geom_tile()` # `&` operator apply it to all plots ggheatmap(small_mat) + anno_top() + align_dendro() & theme(panel.border = element_rect( colour = \"red\", fill = NA, linewidth = unit(2, \"mm\") )) #> → heatmap built with `geom_tile()` # If the active layout is the annotation stack, the `-` operator will only # add the elements to all plots in the active annotation stack: ggheatmap(small_mat) + anno_left(size = 0.2) + align_dendro(aes(color = branch), k = 3L) + align_dendro(aes(color = branch), k = 3L) - # Modify the the color scales of all plots in the left annotation scale_color_brewer(palette = \"Dark2\") #> → heatmap built with `geom_tile()` # If the active layout is the `stack_layout()` itself, `-` # applies the elements to all plots in the layout except the nested # `ggheatmap()`/`quad_layout()`. stack_alignv(small_mat) + align_dendro() + ggtitle(\"I'm from the parent stack\") + ggheatmap() + # remove any active context stack_active() + align_dendro() + ggtitle(\"I'm from the parent stack\") - # Modify the the color scales of all plots in the stack layout except the # heatmap layout scale_color_brewer(palette = \"Dark2\") - # set the background of all plots in the stack layout except the heatmap # layout theme(plot.background = element_rect(fill = \"red\")) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify components of the layout — layout_annotation","title":"Modify components of the layout — layout_annotation","text":"modify theme layout","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify components of the layout — layout_annotation","text":"","code":"layout_annotation(theme = waiver(), ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify components of the layout — layout_annotation","text":"theme theme() object used customize various elements plot, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. ... dots future extensions must empty.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_annotation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Modify components of the layout — layout_annotation","text":"guides, panel.border, background always used even nested alignpatches object. title, subtitle, caption, margins added top-level alignpatches object .","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify components of the layout — layout_annotation","text":"","code":"p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p3 <- ggplot(mtcars) + geom_bar(aes(gear)) + facet_wrap(~cyl) align_plots( p1 + theme(plot.background = element_blank()), p2 + theme(plot.background = element_blank()), p3 + theme(plot.background = element_blank()) ) + layout_annotation( theme = theme(plot.background = element_rect(fill = \"red\")) )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_design.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the grid to compose plots in — layout_design","title":"Define the grid to compose plots in — layout_design","text":"control different plots laid , need add layout design specification. nesting grids, layout scoped current nesting level.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_design.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the grid to compose plots in — layout_design","text":"","code":"layout_design( ncol = waiver(), nrow = waiver(), byrow = waiver(), widths = waiver(), heights = waiver(), design = waiver(), guides = NA )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_design.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the grid to compose plots in — layout_design","text":"ncol, nrow dimensions grid create - NULL use logic facet_wrap() set dimensions byrow FALSE plots filled column-major order. widths, heights relative widths heights column row grid. get repeated match dimensions grid. special value NA behave 1null unit unless fixed aspect plot inserted case allow dimension expand contract match aspect ratio content. design Specification location areas layout. Can either specified text string concatenating calls area() together. guides string one \"t\", \"l\", \"b\", \"r\" indicating side guide legends collected. Defaults waiver(), inherits parent layout. parent layout, NULL provided, guides collected.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_design.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define the grid to compose plots in — layout_design","text":"layout_design object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_design.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define the grid to compose plots in — layout_design","text":"","code":"p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p3 <- ggplot(mtcars) + geom_bar(aes(gear)) + facet_wrap(~cyl) align_plots(p1, p2, p3) + layout_design(nrow = 1L) align_plots(p1, p2, p3) + layout_design(ncol = 1L)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_expand.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Expansion for the Layout — layout_expand","title":"Set Expansion for the Layout — layout_expand","text":"align axes, important keep expansion consistent across plots layout. can add layout_expand object layout. quad_layout() function, must specify x y arguments. layouts, can pass expansion values using ... directly.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_expand.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Expansion for the Layout — layout_expand","text":"","code":"layout_expand(..., x = waiver(), y = waiver())"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_expand.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Expansion for the Layout — layout_expand","text":"... list range expansion constants, used add padding around data ensure placed distance away axes. Use convenience function expansion() generate values. x, y ..., specifically quad_layout().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_title.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate the whole layout — layout_title","title":"Annotate the whole layout — layout_title","text":"Annotate whole layout","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_title.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate the whole layout — layout_title","text":"","code":"layout_title(title = waiver(), subtitle = waiver(), caption = waiver())"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_title.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate the whole layout — layout_title","text":"title text title. subtitle text subtitle plot displayed title. caption text caption displayed bottom-right plot default.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_title.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Annotate the whole layout — layout_title","text":"layout_title object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_title.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Annotate the whole layout — layout_title","text":"","code":"p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p3 <- ggplot(mtcars) + geom_bar(aes(gear)) + facet_wrap(~cyl) align_plots(p1, p2, p3) + layout_title(title = \"I'm title\")"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the links to connect a pair of observations — link_draw","title":"Define the links to connect a pair of observations — link_draw","text":"function allows users define links pair observations, facilitating visualization connections related data points.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the links to connect a pair of observations — link_draw","text":"","code":"link_draw(.draw, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the links to connect a pair of observations — link_draw","text":".draw function used draw links. function must return grob() object. function return valid grob, drawing occur. input data function include data frame coordinates pair observations linked. ... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_line.html","id":null,"dir":"Reference","previous_headings":"","what":"Link the paired observations with a line — link_line","title":"Link the paired observations with a line — link_line","text":"Link paired observations line","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_line.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Link the paired observations with a line — link_line","text":"","code":"link_line(..., .element = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_line.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Link the paired observations with a line — link_line","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. .element element_line() object. Vectorized fields recycled match total number groups, can wrap element () recycle match drawing groups. drawing groups typically correspond product number observations sides, pair observations linked single line.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_tetragon.html","id":null,"dir":"Reference","previous_headings":"","what":"Link the paired observations with a quadrilateral — link_tetragon","title":"Link the paired observations with a quadrilateral — link_tetragon","text":"Link paired observations quadrilateral","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_tetragon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Link the paired observations with a quadrilateral — link_tetragon","text":"","code":"link_tetragon(..., .element = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_tetragon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Link the paired observations with a quadrilateral — link_tetragon","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. .element element_polygon() object. Vectorized fields recycled match total number groups, can wrap element () recycle match drawing groups. drawing groups usually defined groups, differ defined group observations separated linked single quadrilateral. cases, number drawing groups larger number defined groups.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the links to connect the marked observations — mark_draw","title":"Define the links to connect the marked observations — mark_draw","text":"function allows users define links marked observations plot panel (e.g., creating visual connections related data), help explain observations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the links to connect the marked observations — mark_draw","text":"","code":"mark_draw(.draw, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the links to connect the marked observations — mark_draw","text":".draw function used draw links. function must return grob() object. function return valid grob, nothing drawn. input data function must contain two arguments: data frame panel side coordinates data frame marked observation coordinates. ... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_line.html","id":null,"dir":"Reference","previous_headings":"","what":"Link the observations and the panel with a line — mark_line","title":"Link the observations and the panel with a line — mark_line","text":"Link observations panel line","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_line.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Link the observations and the panel with a line — mark_line","text":"","code":"mark_line(..., .element = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_line.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Link the observations and the panel with a line — mark_line","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. .element element_line() object. Vectorized fields recycled match total number groups, can wrap element () recycle match drawing groups. drawing groups typically correspond number observations, observation linked plot panel.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_tetragon.html","id":null,"dir":"Reference","previous_headings":"","what":"Link the observations and the panel with a quadrilateral — mark_tetragon","title":"Link the observations and the panel with a quadrilateral — mark_tetragon","text":"Link observations panel quadrilateral","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_tetragon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Link the observations and the panel with a quadrilateral — mark_tetragon","text":"","code":"mark_tetragon(..., .element = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_tetragon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Link the observations and the panel with a quadrilateral — mark_tetragon","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. .element element_polygon() object. Vectorized fields recycled match total number groups, can wrap element () recycle match drawing groups. drawing groups usually defined groups, differ defined group observations separated linked single quadrilateral. cases, number drawing groups larger number defined groups.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_triangle.html","id":null,"dir":"Reference","previous_headings":"","what":"Link the observations and the panel with a triangle — mark_triangle","title":"Link the observations and the panel with a triangle — mark_triangle","text":"Link observations panel triangle","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_triangle.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Link the observations and the panel with a triangle — mark_triangle","text":"","code":"mark_triangle(..., orientation = \"plot\", .element = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_triangle.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Link the observations and the panel with a triangle — mark_triangle","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. orientation single string, either \"plot\" \"observation\", indicating base triangle. .element element_polygon() object. Vectorized fields recycled match total number groups, can wrap element () recycle match drawing groups. orientation \"plot\", drawing groups typically correspond number observations. orientation \"observation\", drawing groups usually match defined groups, differ defined group observations separated linked single triangle. case, number drawing groups larger number defined groups.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/memo_order.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort matrix for better visualization — memo_order","title":"Sort matrix for better visualization — memo_order","text":"Helper function used order Oncoplot samples. Typically, use combination align_reorder(), e.g., align_reorder(memo_order).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/memo_order.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort matrix for better visualization — memo_order","text":"","code":"memo_order(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/memo_order.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort matrix for better visualization — memo_order","text":"x matrix, NA values treated empty.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/memo_order.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sort matrix for better visualization — memo_order","text":"vector ordering weights.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/new_tune.html","id":null,"dir":"Reference","previous_headings":"","what":"Change the shape of the input object — new_tune","title":"Change the shape of the input object — new_tune","text":"new_tune: Creates new object wrapping scalar list specified attributes class. tune_data: Retrieves original input data.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/new_tune.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change the shape of the input object — new_tune","text":"","code":"new_tune(x, ..., class = character()) tune_data(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/new_tune.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change the shape of the input object — new_tune","text":"x R object. ... Additional attributes passed structure(). class character vector specifying class name added.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/no_expansion.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove scale expansion — no_expansion","title":"Remove scale expansion — no_expansion","text":"Remove scale expansion","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/no_expansion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove scale expansion — no_expansion","text":"","code":"no_expansion(borders = \"tlbr\")"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/no_expansion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove scale expansion — no_expansion","text":"borders border removed? string containing one \"t\", \"l\", \"b\", \"r\", \"x\", \"y\".","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/no_expansion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove scale expansion — no_expansion","text":"object can added ggplot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/order2.html","id":null,"dir":"Reference","previous_headings":"","what":"Ordering Permutation — order2","title":"Ordering Permutation — order2","text":"order2 returns permutation rearranges first argument ascending order.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/order2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ordering Permutation — order2","text":"","code":"order2(x) # S3 method for class 'hclust' order2(x) # S3 method for class 'dendrogram' order2(x) # S3 method for class 'ser_permutation_vector' order2(x) # S3 method for class 'ser_permutation' order2(x) # S3 method for class 'phylo' order2(x) # S3 method for class 'memo_weights' order2(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/order2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ordering Permutation — order2","text":"x objects can extracting ordering.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/order2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ordering Permutation — order2","text":"integer vector unless inputs 2^31 elements, double vector.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/order2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Ordering Permutation — order2","text":"","code":"order2(hclust2(matrix(rnorm(100L), nrow = 10L))) #> [1] 5 6 2 3 9 1 4 8 7 10"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/pair_links.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create pairs of observation groups — pair_links","title":"Helper function to create pairs of observation groups — pair_links","text":"ggmark() cross_link() allow users add links observations. functions help define linked observations. selected pairs either linked together, group pair linked separately plot area. pair_links: Helper function create pairs observation groups. range_link: Helper function create range observations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/pair_links.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create pairs of observation groups — pair_links","text":"","code":"pair_links(..., .handle_missing = \"error\", .reorder = NULL) range_link(point1, point2)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/pair_links.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create pairs of observation groups — pair_links","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. .handle_missing string \"error\" \"remove\" indicates action handling missing observations. .reorder string \"hand1\" \"hand2\" indicating whether reorder input links follow specified layout ordering. point1, point2 single integer character index, defining lower higher bounds range. integer indices, wrap () indicate ordered index layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/pair_links.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create pairs of observation groups — pair_links","text":"","code":"x <- pair_links( # group on the left hand only c(\"a\", \"b\"), # normally, integer index will be interpreted as the index of the # origianl data 1:2, # wrapped with `I()` indicate` the integer index is ordering of the # layout I(1:2), range_link(1, 6), range_link(\"a\", \"b\"), # group on the right hand only ~ 1:2, ~ c(\"a\", \"b\"), ~ range_link(1, 6), # group on the both side range_link(1, 6) ~ c(\"a\", \"b\"), # waiver() indicates the right hand is the same of the left hand range_link(1, 6) ~ waiver(), # the same for the left hand waiver() ~ 1:2, ~NULL # an empty link ) x #> #> A total of 12 pairs of link groups #> #> hand1 ~ hand2 #> 1: c(\"a\", \"b\") ~ #> 2: 1:2 ~ #> 3: I(1:2) ~ #> 4: range_link(1, 6) ~ #> 5: range_link(\"a\", \"b\") ~ #> 6: ~ 1:2 #> 7: ~ c(\"a\", \"b\") #> 8: ~ range_link(1, 6) #> 9: range_link(1, 6) ~ c(\"a\", \"b\") #> 10: range_link(1, 6) ~ waiver() #> 11: waiver() ~ 1:2 #> 12: ~ #> #> A total of 14 link groups # we can modify it as usual list x[[1]] <- NULL # remove the first link x$a <- ~LETTERS x #> #> A total of 12 pairs of link groups #> #> hand1 ~ hand2 #> 1: 1:2 ~ #> 2: I(1:2) ~ #> 3: range_link(1, 6) ~ #> 4: range_link(\"a\", \"b\") ~ #> 5: ~ 1:2 #> 6: ~ c(\"a\", \"b\") #> 7: ~ range_link(1, 6) #> 8: range_link(1, 6) ~ c(\"a\", \"b\") #> 9: range_link(1, 6) ~ waiver() #> 10: waiver() ~ 1:2 #> 11: ~ #> a: ~ c(A, B, ..., Z) #> #> A total of 14 link groups # modify with a list x[1:2] <- list(~ c(\"a\", \"b\"), ~ range_link(\"a\", \"b\")) x #> #> A total of 12 pairs of link groups #> #> hand1 ~ hand2 #> 1: ~ c(\"a\", \"b\") #> 2: ~ range_link(\"a\", \"b\") #> 3: range_link(1, 6) ~ #> 4: range_link(\"a\", \"b\") ~ #> 5: ~ 1:2 #> 6: ~ c(\"a\", \"b\") #> 7: ~ range_link(1, 6) #> 8: range_link(1, 6) ~ c(\"a\", \"b\") #> 9: range_link(1, 6) ~ waiver() #> 10: waiver() ~ 1:2 #> 11: ~ #> a: ~ c(A, B, ..., Z) #> #> A total of 14 link groups"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.Heatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.Heatmap","title":"Convert Object into a Grob — patch.Heatmap","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.Heatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.Heatmap","text":"","code":"# S3 method for class 'Heatmap' patch(x, ..., device = NULL) # S3 method for class 'HeatmapList' patch(x, ..., device = NULL) # S3 method for class 'HeatmapAnnotation' patch(x, ..., device = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.Heatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.Heatmap","text":"x object converted grob. ... Additional arguments passed draw(). device function opens graphics device temporary rendering. default -screen, -memory device based pdf device, default device may satisfactory using custom fonts.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.Heatmap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.Heatmap","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.alignpatches.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.alignpatches","title":"Convert Object into a Grob — patch.alignpatches","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.alignpatches.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.alignpatches","text":"","code":"# S3 method for class 'alignpatches' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.alignpatches.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.alignpatches","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.alignpatches.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.alignpatches","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.formula.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.formula","title":"Convert Object into a Grob — patch.formula","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.formula.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.formula","text":"","code":"# S3 method for class 'formula' patch(x, ..., device = NULL, name = NULL) # S3 method for class '`function`' patch(x, ..., device = NULL, name = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.formula.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.formula","text":"x object converted grob. ... Graphical Parameters passed par(). device function opens graphics device grid.echo() work . default -screen, -memory device based pdf device. default device may satisfactory using custom fonts. name character identifier.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.formula.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.formula","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.ggplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.ggplot","title":"Convert Object into a Grob — patch.ggplot","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.ggplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.ggplot","text":"","code":"# S3 method for class 'ggplot' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.ggplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.ggplot","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.ggplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.ggplot","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.grob","title":"Convert Object into a Grob — patch.grob","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.grob","text":"","code":"# S3 method for class 'grob' patch(x, ...) # S3 method for class 'gList' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.grob","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.grob","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch","title":"Convert Object into a Grob — patch","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch","text":"","code":"patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch","text":"x object converted grob. ... Additional arguments passed specific methods.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.patch","title":"Convert Object into a Grob — patch.patch","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.patch","text":"","code":"# S3 method for class 'patch' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.patch","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.patch","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch_ggplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.patch_ggplot","title":"Convert Object into a Grob — patch.patch_ggplot","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch_ggplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.patch_ggplot","text":"","code":"# S3 method for class 'patch_ggplot' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch_ggplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.patch_ggplot","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch_ggplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.patch_ggplot","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patchwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.patchwork","title":"Convert Object into a Grob — patch.patchwork","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patchwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.patchwork","text":"","code":"# S3 method for class 'patchwork' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patchwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.patchwork","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patchwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.patchwork","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.pheatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.pheatmap","title":"Convert Object into a Grob — patch.pheatmap","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.pheatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.pheatmap","text":"","code":"# S3 method for class 'pheatmap' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.pheatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.pheatmap","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.pheatmap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.pheatmap","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.recordedplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.recordedplot","title":"Convert Object into a Grob — patch.recordedplot","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.recordedplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.recordedplot","text":"","code":"# S3 method for class 'recordedplot' patch(x, ..., device = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.recordedplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.recordedplot","text":"x object converted grob. ... used currently. device function opens graphics device grid.echo() work . default -screen, -memory device based pdf device. default device may satisfactory using custom fonts.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.recordedplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.recordedplot","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.trellis.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.trellis","title":"Convert Object into a Grob — patch.trellis","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.trellis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.trellis","text":"","code":"# S3 method for class 'trellis' patch(x, ..., device = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.trellis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.trellis","text":"x object converted grob. ... Arguments passed grid::grid.grabExpr warn integer specifying amount warnings emit. 0 means warnings, 1 means warn certain grab faithfully represent original scene. 2 means warn possibility grab faithfully represent original scene. wrap logical indicating output captured. TRUE, non-grob element display list captured wrapping grob. wrap.grobs logical indicating whether, wrapping elements (wrap=TRUE), wrap grobs (just wrap viewports). width,height Size device used temporary rendering. device function opens graphics device temporary rendering. default -screen, -memory device based pdf device, default device may satisfactory using custom fonts.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.trellis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.trellis","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":null,"dir":"Reference","previous_headings":"","what":"Add patch titles to plot borders — patch_titles","title":"Add patch titles to plot borders — patch_titles","text":"function extends ggplot2's title functionality, allowing add titles border plot: top, left, bottom, right.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add patch titles to plot borders — patch_titles","text":"","code":"patch_titles( top = waiver(), left = waiver(), bottom = waiver(), right = waiver() )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add patch titles to plot borders — patch_titles","text":"top, left, bottom, right string specifying title added top, left, bottom, right border plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add patch titles to plot borders — patch_titles","text":"labels object added ggplot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add patch titles to plot borders — patch_titles","text":"appearance alignment patch titles can customized using theme(): plot.patch_title/plot.patch_title.*: Controls text appearance patch titles. default, plot.patch_title inherit plot.title, settings border inherit plot.patch_title, exception angle property, inherited. plot.patch_title.position/plot.patch_title.position.*: Determines alignment patch titles. default, plot.patch_title.position inherit plot.title.position, settings border inherit plot.patch_title. value \"panel\" aligns patch titles plot panels. Setting \"plot\" aligns patch title entire plot (excluding margins plot tags).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add patch titles to plot borders — patch_titles","text":"","code":"ggplot(mtcars) + geom_point(aes(mpg, disp)) + patch_titles( top = \"I'm top patch title\", left = \"I'm left patch title\", bottom = \"I'm bottom patch title\", right = \"I'm right patch title\" )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/plus-ggalign_plot-ANY-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Add custom objects to ggalign plot — +,ggalign_plot,ANY-method","title":"Add custom objects to ggalign plot — +,ggalign_plot,ANY-method","text":"Add custom objects ggalign plot","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/plus-ggalign_plot-ANY-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add custom objects to ggalign plot — +,ggalign_plot,ANY-method","text":"","code":"# S4 method for class 'ggalign_plot,ANY' e1 + e2"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_active.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine the Active Context of Quad-Layout — quad_active","title":"Determine the Active Context of Quad-Layout — quad_active","text":"quad_active: Sets active context quad_layout()/ggheatmap() . quad_anno: Sets active context specified annotation stack based position argument. anno_top: special case quad_anno position = \"top\". anno_left: special case quad_anno position = \"left\". anno_bottom: special case quad_anno position = \"bottom\". anno_right: special case quad_anno position = \"right\".","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_active.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the Active Context of Quad-Layout — quad_active","text":"","code":"quad_active(width = NULL, height = NULL) quad_anno( position, size = NULL, free_guides = waiver(), initialize = NULL, what = waiver() ) anno_top( size = NULL, free_guides = waiver(), initialize = NULL, what = waiver() ) anno_left( size = NULL, free_guides = waiver(), initialize = NULL, what = waiver() ) anno_bottom( size = NULL, free_guides = waiver(), initialize = NULL, what = waiver() ) anno_right( size = NULL, free_guides = waiver(), initialize = NULL, what = waiver() )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_active.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the Active Context of Quad-Layout — quad_active","text":"width, height relative width/height main plot, can unit object. position string \"top\", \"left\", \"bottom\", \"right\" indicates annotation stack activated. size numeric value unit object set total height/width annotation stack. position \"top\" \"bottom\", size sets total height annotation. position \"left\" \"right\", size sets total width annotation. free_guides Override guides collection behavior specified quad_layout()/ggheatmap() annotation stack. initialize boolean indicating whether annotation stack initialized already. default, annotation stack layout attempt initialize data compatible. set TRUE, data quad_layout()/ggheatmap() incompatible annotation stack, data used stack. get activated annotation stack? single number string plot elements layout. NULL, remove active context.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_active.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the Active Context of Quad-Layout — quad_active","text":"object can added quad_layout()/ggheatmap().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_active.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine the Active Context of Quad-Layout — quad_active","text":"default, quad_anno() attempts initialize annotation stack layout using data quad_layout()/ggheatmap(). However, situations want use different data annotation stack, can set initialize = FALSE provide custom stack_layout().","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_init.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize Quad-Layout Annotation — quad_init","title":"Initialize Quad-Layout Annotation — quad_init","text":"function deprecated, can add stack_layout() directly.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_init.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize Quad-Layout Annotation — quad_init","text":"","code":"quad_init(position, data = waiver(), ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange plots in the quad-side of a main plot — quad_layout","title":"Arrange plots in the quad-side of a main plot — quad_layout","text":"function arranges plots around quad-sides main plot, aligning horizontal vertical axes, can handle either discrete continuous variables. xlim provided, continuous variable required aligned vertical direction. Otherwise, discrete variable required aligned. ylim provided, continuous variable required aligned horizontal direction. Otherwise, discrete variable required aligned. quad_discrete special case xlim ylim provided. quad_continuous special case xlim ylim provided. historical reasons, following aliases available: quad_alignh: Align discrete variables horizontal direction continuous variables vertical direction. quad_alignv: Align discrete variables vertical direction continuous variables horizontal direction. quad_alignb alias quad_discrete. quad_free alias quad_continuous.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange plots in the quad-side of a main plot — quad_layout","text":"","code":"quad_layout( data = waiver(), mapping = aes(), xlim = waiver(), ylim = waiver(), ..., theme = NULL, active = NULL, width = NA, height = NA ) quad_alignh(..., ylim = waiver()) quad_alignv(..., xlim = waiver()) quad_discrete( data = waiver(), mapping = aes(), ..., theme = NULL, active = NULL, width = NA, height = NA ) quad_continuous( data = waiver(), mapping = aes(), xlim = NULL, ylim = NULL, ..., theme = NULL, active = NULL, width = NA, height = NA )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange plots in the quad-side of a main plot — quad_layout","text":"data Default dataset use layout. specified, must supplied plot added layout. default, attempt inherit parent layout. xlim ylim provided, data frame required, fortify_data_frame() used convert data data frame. inherited annotation stack, transposition applied. Otherwise, matrix required, fortify_matrix() used convert data matrix. inherited column annotation stack, data transposed. mapping Default list aesthetic mappings use main plot layout. specified, must supplied layer added main plot. xlim, ylim continuous_limits() object specifying left/lower limit right/upper limit scale. Used align continuous axis. ... Additional arguments passed fortify_data_frame() fortify_matrix(). theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. active active() object defines context settings added layout. width, height relative width/height main plot, can unit object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange plots in the quad-side of a main plot — quad_layout","text":"QuadLayout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_layout.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Arrange plots in the quad-side of a main plot — quad_layout","text":"either xlim ylim provided, data input converted matrix using fortify_matrix(), data underlying main plot contain following columns: .panel_x .panel_y: column row panel groups. .x .y: integer index x y coordinates .discrete_x .discrete_y: factor data labels (applicable .row_names .column_names exists). .row_names .column_names: character row column names original matrix (applicable names exist). .row_index .column_index: row column index original matrix. value: actual matrix value. Otherwise, data input used main plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_switch.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine the Active Context of Quad-Layout — quad_switch","title":"Determine the Active Context of Quad-Layout — quad_switch","text":"quad_switch() integrates quad_active() quad_anno() one function ease use. function allows quickly change active context quad_layout() annotations. hmanno alias quad_switch, additional arguments backward compatibility","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_switch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the Active Context of Quad-Layout — quad_switch","text":"","code":"quad_switch( position = NULL, size = NULL, width = NULL, height = NULL, free_guides = waiver(), initialize = NULL, what = waiver() ) hmanno( position = NULL, size = NULL, width = NULL, height = NULL, free_guides = waiver(), initialize = NULL, what = waiver() )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_switch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the Active Context of Quad-Layout — quad_switch","text":"position string \"top\", \"left\", \"bottom\", \"right\" indicates annotation stack activated. NULL, sets active context quad_layout()/ggheatmap() . size numeric value unit object set total height/width annotation stack. position \"top\" \"bottom\", size sets total height annotation. position \"left\" \"right\", size sets total width annotation. width, height relative width/height main plot, can unit object. free_guides Override guides collection behavior specified quad_layout()/ggheatmap() annotation stack. initialize boolean indicating whether annotation stack initialized already. default, annotation stack layout attempt initialize data compatible. set TRUE, data quad_layout()/ggheatmap() incompatible annotation stack, data used stack. get activated annotation stack? single number string plot elements layout. NULL, remove active context.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_switch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the Active Context of Quad-Layout — quad_switch","text":"object can added quad_layout()/ggheatmap().","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_switch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine the Active Context of Quad-Layout — quad_switch","text":"","code":"ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + align_dendro() #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick.html","id":null,"dir":"Reference","previous_headings":"","what":"Rasterize the input object — raster_magick","title":"Rasterize the input object — raster_magick","text":"function rasterizes input graphical objects (e.g., grob, layer, ggplot) optionally processes resulting raster using magick, powerful image manipulation library. allows advanced graphical transformations directly within plotting pipeline.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rasterize the input object — raster_magick","text":"","code":"raster_magick(x, magick = NULL, ..., res = NULL, interpolate = FALSE)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rasterize the input object — raster_magick","text":"x object rasterize, can grob(), layer(), ggplot(), list objects. magick function (purrr-style formula accepted) takes image_read() object input returns object compatible .raster(). can use image_*() functions magick package process raster image. ... used currently. res integer sets desired resolution pixels. interpolate logical value indicating whether linearly interpolate image (alternative use nearest-neighbour interpolation, gives blocky result).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rasterize the input object — raster_magick","text":"object class input.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Rasterize the input object — raster_magick","text":"","code":"# data generated code was copied from `ComplexHeatmap` set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) rownames(small_mat) <- paste0(\"row\", seq_len(nrow(small_mat))) colnames(small_mat) <- paste0(\"column\", seq_len(ncol(small_mat))) ggheatmap(small_mat, aes(.x, .y), filling = NULL) + raster_magick(geom_tile(aes(fill = value)), res = 20) ggheatmap(small_mat, aes(.x, .y), filling = NULL) + # Use `magick::filter_types()` to check available `filter` arguments raster_magick(geom_tile(aes(fill = value)), magick = function(image) { magick::image_resize(image, geometry = \"50%x\", filter = \"Lanczos\" ) } )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick_interal.html","id":null,"dir":"Reference","previous_headings":"","what":"Rasterize the input object — raster_magick_interal","title":"Rasterize the input object — raster_magick_interal","text":"internal function designed implement functionality raster_magick(). assumes input arguments valid perform additional checks.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick_interal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rasterize the input object — raster_magick_interal","text":"","code":".raster_magick(x, ...) # S3 method for class 'Layer' .raster_magick(x, ...) # S3 method for class 'list' .raster_magick(x, ...) # S3 method for class 'ggplot' .raster_magick(x, ...) # S3 method for class 'grob' .raster_magick(x, magick = NULL, ..., res = NULL, interpolate = FALSE) # S3 method for class 'gList' .raster_magick(x, magick = NULL, ..., res = NULL, interpolate = FALSE) # S3 method for class 'ggalignRasterMagick' .raster_magick(x, magick = NULL, ..., res = NULL, interpolate = FALSE) # S3 method for class 'zeroGrob' .raster_magick(x, ...) # Default S3 method .raster_magick(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick_interal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rasterize the input object — raster_magick_interal","text":"x object rasterize, can grob(), layer(), ggplot(), list objects. ... used currently. magick function (purrr-style formula accepted) takes image_read() object input returns object compatible .raster(). can use image_*() functions magick package process raster image. res integer sets desired resolution pixels. interpolate logical value indicating whether linearly interpolate image (alternative use nearest-neighbour interpolation, gives blocky result).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick_interal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rasterize the input object — raster_magick_interal","text":"object class input.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/read_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Example Data — read_example","title":"Read Example Data — read_example","text":"function reads example data file. file specified, returns list available example files.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/read_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Example Data — read_example","text":"","code":"read_example(file = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/read_example.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Example Data — read_example","text":"file string representing name example file read. NULL, function return list available example file names.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/read_example.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Example Data — read_example","text":"file NULL, returns character vector available example file names. Otherwise, returns contents specified example file, read R object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/read_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Example Data — read_example","text":"","code":"read_example() #> [1] \"gene_expression.rds\" \"measles.rds\""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. grid gpar, unit","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scale_draw_manual.html","id":null,"dir":"Reference","previous_headings":"","what":"Scale for draw aesthetic — scale_draw_manual","title":"Scale for draw aesthetic — scale_draw_manual","text":"Draw ggplot2 layer using grob function.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scale_draw_manual.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Scale for draw aesthetic — scale_draw_manual","text":"","code":"scale_draw_manual( ..., values, aesthetics = \"draw\", breaks = waiver(), na.value = NA )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scale_draw_manual.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scale for draw aesthetic — scale_draw_manual","text":"... Arguments passed ggplot2::discrete_scale name name scale. Used axis legend title. waiver(), default, name scale taken first mapping used aesthetic. NULL, legend title omitted. labels One : NULL labels waiver() default labels computed transformation object character vector giving labels (must length breaks) expression vector (must length breaks). See ?plotmath details. function takes breaks input returns labels output. Also accepts rlang lambda function notation. limits One : NULL use default scale values character vector defines possible values scale order function accepts existing (automatic) values returns new ones. Also accepts rlang lambda function notation. na.translate Unlike continuous scales, discrete scales can easily show missing values, default. want remove missing values discrete scale, specify na.translate = FALSE. drop unused factor levels omitted scale? default, TRUE, uses levels appear data; FALSE includes levels factor. Please note display every level legend, layer use show.legend = TRUE. guide function used create guide name. See guides() information. call call used construct scale reporting messages. super super class use constructed scale values list functions (including purrr-like lambda syntax) define cell's grob (graphical object) drawn. aesthetics Character string vector character strings listing name(s) aesthetic(s) scale works . can useful, example, apply colour settings colour fill aesthetics time, via aesthetics = c(\"colour\", \"fill\"). breaks One : NULL breaks waiver() default breaks (scale limits) character vector breaks function takes limits input returns breaks output na.value aesthetic value use missing (NA) values","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scale_draw_manual.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Scale for draw aesthetic — scale_draw_manual","text":"want combine functionality multiple geoms, can typically achieved preparing data geom inside draw_*() call sending different geoms, collecting output grid::gList (list grobs) draw_group() grid::gTree (grob containing multiple child grobs) draw_panel().","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scale_draw_manual.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Scale for draw aesthetic — scale_draw_manual","text":"","code":"text <- grid::textGrob( \"ggdraw\", x = c(0, 0, 0.5, 1, 1), y = c(0, 1, 0.5, 0, 1), hjust = c(0, 0, 0.5, 1, 1), vjust = c(0, 1, 0.5, 0, 1) ) ggplot(data.frame(x = 1, y = 2)) + geom_draw(text)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_align.html","id":null,"dir":"Reference","previous_headings":"","what":"Align Specifications in the Layout — scheme_align","title":"Align Specifications in the Layout — scheme_align","text":"scheme_align() function defines align Specifications plots.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_align.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Align Specifications in the Layout — scheme_align","text":"","code":"scheme_align(guides = NA, free_spaces = NA, free_labs = NA)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_align.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Align Specifications in the Layout — scheme_align","text":"guides string one \"t\", \"l\", \"b\", \"r\" indicating side guide legends collected. Defaults waiver(), inherits parent layout. parent layout, guides collected. NULL, guides collected. free_spaces string one \"t\", \"l\", \"b\", \"r\" indicating border spaces removed. Defaults waiver(), inherits parent layout. parent, default NULL, meaning spaces removed. Usually want apply whole layout, instead individual plots. free_labs string one \"t\", \"l\", \"b\", \"r\" indicating axis titles free alignment. Defaults waiver(), inherits parent layout. parent layout, axis titles aligned. NULL, axis titles aligned.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_align.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Align Specifications in the Layout — scheme_align","text":"scheme_align object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_align.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Align Specifications in the Layout — scheme_align","text":"","code":"set.seed(123) mat <- matrix(rnorm(72), nrow = 8) # used in the layout, define the default action for all plots in the layout ggheatmap(mat) - scheme_align(guides = NULL) + anno_right() + align_dendro(aes(color = branch), k = 3) #> → heatmap built with `geom_tile()` # You can also add it for a single plot ggheatmap(mat) - # for all plots in the layout, we default won't collect any guide legends scheme_align(guides = NULL) + # for the heatmap body, we collect guide legends in the right # note, the guide legends will be collected to the right side of the # layout which will overlap the legends in the right annotation scheme_align(guides = \"r\") + anno_right() + align_dendro(aes(color = branch), k = 3) #> → heatmap built with `geom_tile()` # to avoid overlapping, we can also collect the guide legends in the # right annotation ggheatmap(mat) - scheme_align(guides = NULL) + scheme_align(guides = \"r\") + anno_right() + align_dendro(aes(color = branch), k = 3) + scheme_align(guides = \"r\") #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot data Specifications — scheme_data","title":"Plot data Specifications — scheme_data","text":"Transforms plot data. Many functions package require specific data format align observations, scheme_data() helps reformat data frames needed.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot data Specifications — scheme_data","text":"","code":"scheme_data(data, inherit = FALSE)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot data Specifications — scheme_data","text":"data function transform plot data rendering. Acceptable values include: NULL: action taken. waiver(): Inherits parent layout. function purrr-style formula: Used transform plot data, accept data frame return data frame. can apply parent layout scheme_data function, using inherit argument. Use hook modify data geoms layout created (matrix data, melted long format data frame) rendering ggplot2. returned data must data frame ggplot. inherit single boolean value indicates whether apply parent scheme_data first apply specified scheme_data plot. Defaults FALSE.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot data Specifications — scheme_data","text":"Defaults attempt inherit parent layout actual data inherited parent layout, one exception: align_dendro(), inherit scheme_data default.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_theme.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot default theme — scheme_theme","title":"Plot default theme — scheme_theme","text":"scheme_theme() serves default theme always overridden theme() settings applied directly plot. default theme (scheme_theme()) applied first, followed specific theme() settings, even theme() added scheme_theme().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_theme.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot default theme — scheme_theme","text":"","code":"scheme_theme( ..., line, rect, text, title, aspect.ratio, axis.title, axis.title.x, axis.title.x.top, axis.title.x.bottom, axis.title.y, axis.title.y.left, axis.title.y.right, axis.text, axis.text.x, axis.text.x.top, axis.text.x.bottom, axis.text.y, axis.text.y.left, axis.text.y.right, axis.text.theta, axis.text.r, axis.ticks, axis.ticks.x, axis.ticks.x.top, axis.ticks.x.bottom, axis.ticks.y, axis.ticks.y.left, axis.ticks.y.right, axis.ticks.theta, axis.ticks.r, axis.minor.ticks.x.top, axis.minor.ticks.x.bottom, axis.minor.ticks.y.left, axis.minor.ticks.y.right, axis.minor.ticks.theta, axis.minor.ticks.r, axis.ticks.length, axis.ticks.length.x, axis.ticks.length.x.top, axis.ticks.length.x.bottom, axis.ticks.length.y, axis.ticks.length.y.left, axis.ticks.length.y.right, axis.ticks.length.theta, axis.ticks.length.r, axis.minor.ticks.length, axis.minor.ticks.length.x, axis.minor.ticks.length.x.top, axis.minor.ticks.length.x.bottom, axis.minor.ticks.length.y, axis.minor.ticks.length.y.left, axis.minor.ticks.length.y.right, axis.minor.ticks.length.theta, axis.minor.ticks.length.r, axis.line, axis.line.x, axis.line.x.top, axis.line.x.bottom, axis.line.y, axis.line.y.left, axis.line.y.right, axis.line.theta, axis.line.r, legend.background, legend.margin, legend.spacing, legend.spacing.x, legend.spacing.y, legend.key, legend.key.size, legend.key.height, legend.key.width, legend.key.spacing, legend.key.spacing.x, legend.key.spacing.y, legend.frame, legend.ticks, legend.ticks.length, legend.axis.line, legend.text, legend.text.position, legend.title, legend.title.position, legend.position, legend.position.inside, legend.direction, legend.byrow, legend.justification, legend.justification.top, legend.justification.bottom, legend.justification.left, legend.justification.right, legend.justification.inside, legend.location, legend.box, legend.box.just, legend.box.margin, legend.box.background, legend.box.spacing, panel.background, panel.border, panel.spacing, panel.spacing.x, panel.spacing.y, panel.grid, panel.grid.major, panel.grid.minor, panel.grid.major.x, panel.grid.major.y, panel.grid.minor.x, panel.grid.minor.y, panel.ontop, plot.background, plot.title, plot.title.position, plot.subtitle, plot.caption, plot.caption.position, plot.tag, plot.tag.position, plot.tag.location, plot.margin, strip.background, strip.background.x, strip.background.y, strip.clip, strip.placement, strip.text, strip.text.x, strip.text.x.bottom, strip.text.x.top, strip.text.y, strip.text.y.left, strip.text.y.right, strip.switch.pad.grid, strip.switch.pad.wrap, complete = FALSE, validate = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_theme.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot default theme — scheme_theme","text":"... theme() object additional element specifications part base ggplot2. general, also defined element tree argument. Splicing list also supported. line line elements (element_line()) rect rectangular elements (element_rect()) text text elements (element_text()) title title elements: plot, axes, legends (element_text(); inherits text) aspect.ratio aspect ratio panel axis.title, axis.title.x, axis.title.y, axis.title.x.top, axis.title.x.bottom, axis.title.y.left, axis.title.y.right labels axes (element_text()). Specify axes' labels (axis.title), labels plane (using axis.title.x axis.title.y), individually axis (using axis.title.x.bottom, axis.title.x.top, axis.title.y.left, axis.title.y.right). axis.title.*.* inherits axis.title.* inherits axis.title, turn inherits text axis.text, axis.text.x, axis.text.y, axis.text.x.top, axis.text.x.bottom, axis.text.y.left, axis.text.y.right, axis.text.theta, axis.text.r tick labels along axes (element_text()). Specify axis tick labels (axis.text), tick labels plane (using axis.text.x axis.text.y), individually axis (using axis.text.x.bottom, axis.text.x.top, axis.text.y.left, axis.text.y.right). axis.text.*.* inherits axis.text.* inherits axis.text, turn inherits text axis.ticks, axis.ticks.x, axis.ticks.x.top, axis.ticks.x.bottom, axis.ticks.y, axis.ticks.y.left, axis.ticks.y.right, axis.ticks.theta, axis.ticks.r tick marks along axes (element_line()). Specify tick marks (axis.ticks), ticks plane (using axis.ticks.x axis.ticks.y), individually axis (using axis.ticks.x.bottom, axis.ticks.x.top, axis.ticks.y.left, axis.ticks.y.right). axis.ticks.*.* inherits axis.ticks.* inherits axis.ticks, turn inherits line axis.minor.ticks.x.top, axis.minor.ticks.x.bottom, axis.minor.ticks.y.left, axis.minor.ticks.y.right, axis.minor.ticks.theta, axis.minor.ticks.r minor tick marks along axes (element_line()). axis.minor.ticks.*.* inherit corresponding major ticks axis.ticks.*.*. axis.ticks.length, axis.ticks.length.x, axis.ticks.length.x.top, axis.ticks.length.x.bottom, axis.ticks.length.y, axis.ticks.length.y.left, axis.ticks.length.y.right, axis.ticks.length.theta, axis.ticks.length.r length tick marks (unit) axis.minor.ticks.length, axis.minor.ticks.length.x, axis.minor.ticks.length.x.top, axis.minor.ticks.length.x.bottom, axis.minor.ticks.length.y, axis.minor.ticks.length.y.left, axis.minor.ticks.length.y.right, axis.minor.ticks.length.theta, axis.minor.ticks.length.r length minor tick marks (unit), relative axis.ticks.length provided rel(). axis.line, axis.line.x, axis.line.x.top, axis.line.x.bottom, axis.line.y, axis.line.y.left, axis.line.y.right, axis.line.theta, axis.line.r lines along axes (element_line()). Specify lines along axes (axis.line), lines plane (using axis.line.x axis.line.y), individually axis (using axis.line.x.bottom, axis.line.x.top, axis.line.y.left, axis.line.y.right). axis.line.*.* inherits axis.line.* inherits axis.line, turn inherits line legend.background background legend (element_rect(); inherits rect) legend.margin margin around legend (margin()) legend.spacing, legend.spacing.x, legend.spacing.y spacing legends (unit). legend.spacing.x & legend.spacing.y inherit legend.spacing can specified separately legend.key background underneath legend keys (element_rect(); inherits rect) legend.key.size, legend.key.height, legend.key.width size legend keys (unit); key background height & width inherit legend.key.size can specified separately legend.key.spacing, legend.key.spacing.x, legend.key.spacing.y spacing legend keys given unit. Spacing horizontal (x) vertical (y) direction inherit legend.key.spacing can specified separately. legend.frame frame drawn around bar (element_rect()). legend.ticks tick marks shown along bars axes (element_line()) legend.ticks.length length tick marks legend (unit) legend.axis.line lines along axes legends (element_line()) legend.text legend item labels (element_text(); inherits text) legend.text.position placement legend text relative legend keys bars (\"top\", \"right\", \"bottom\" \"left\"). legend text placement might incompatible legend's direction guides. legend.title title legend (element_text(); inherits title) legend.title.position placement legend title relative main legend (\"top\", \"right\", \"bottom\" \"left\"). legend.position default position legends (\"none\", \"left\", \"right\", \"bottom\", \"top\", \"inside\") legend.position.inside numeric vector length two setting placement legends \"inside\" position. legend.direction layout items legends (\"horizontal\" \"vertical\") legend.byrow whether legend-matrix filled columns (FALSE, default) rows (TRUE). legend.justification anchor point positioning legend inside plot (\"center\" two-element numeric vector) justification according plot area positioned outside plot legend.justification.top, legend.justification.bottom, legend.justification.left, legend.justification.right, legend.justification.inside legend.justification specified per legend.position option. legend.location Relative placement legends outside plot string. Can \"panel\" (default) align legends panels \"plot\" align legends plot whole. legend.box arrangement multiple legends (\"horizontal\" \"vertical\") legend.box.just justification legend within overall bounding box, multiple legends (\"top\", \"bottom\", \"left\", \"right\") legend.box.margin margins around full legend area, specified using margin() legend.box.background background legend area (element_rect(); inherits rect) legend.box.spacing spacing plotting area legend box (unit) panel.background background plotting area, drawn underneath plot (element_rect(); inherits rect) panel.border border around plotting area, drawn top plot covers tick marks grid lines. used fill = NA (element_rect(); inherits rect) panel.spacing, panel.spacing.x, panel.spacing.y spacing facet panels (unit). panel.spacing.x & panel.spacing.y inherit panel.spacing can specified separately. panel.grid, panel.grid.major, panel.grid.minor, panel.grid.major.x, panel.grid.major.y, panel.grid.minor.x, panel.grid.minor.y grid lines (element_line()). Specify major grid lines, minor grid lines separately (using panel.grid.major panel.grid.minor) individually axis (using panel.grid.major.x, panel.grid.minor.x, panel.grid.major.y, panel.grid.minor.y). Y axis grid lines horizontal x axis grid lines vertical. panel.grid.*.* inherits panel.grid.* inherits panel.grid, turn inherits line panel.ontop option place panel (background, gridlines) data layers (logical). Usually used transparent blank panel.background. plot.background background entire plot (element_rect(); inherits rect) plot.title plot title (text appearance) (element_text(); inherits title) left-aligned default plot.title.position, plot.caption.position Alignment plot title/subtitle caption. setting plot.title.position applies title subtitle. value \"panel\" (default) means titles /caption aligned plot panels. value \"plot\" means titles /caption aligned entire plot (minus space margins plot tag). plot.subtitle plot subtitle (text appearance) (element_text(); inherits title) left-aligned default plot.caption caption plot (text appearance) (element_text(); inherits title) right-aligned default plot.tag upper-left label identify plot (text appearance) (element_text(); inherits title) left-aligned default plot.tag.position position tag string (\"topleft\", \"top\", \"topright\", \"left\", \"right\", \"bottomleft\", \"bottom\", \"bottomright\") coordinate. coordinate, can numeric vector length 2 set x,y-coordinate relative whole plot. coordinate option unavailable plot.tag.location = \"margin\". plot.tag.location placement tag string, one \"panel\", \"plot\" \"margin\". Respectively, place tag inside panel space, anywhere plot whole, margin around panel space. plot.margin margin around entire plot (unit sizes top, right, bottom, left margins) strip.background, strip.background.x, strip.background.y background facet labels (element_rect(); inherits rect). Horizontal facet background (strip.background.x) & vertical facet background (strip.background.y) inherit strip.background can specified separately strip.clip strip background edges strip labels clipped extend strip background? Options \"\" clip, \"\" disable clipping \"inherit\" (default) take clipping setting parent viewport. strip.placement placement strip respect axes, either \"inside\" \"outside\". important axes strips side plot. strip.text, strip.text.x, strip.text.y, strip.text.x.top, strip.text.x.bottom, strip.text.y.left, strip.text.y.right facet labels (element_text(); inherits text). Horizontal facet labels (strip.text.x) & vertical facet labels (strip.text.y) inherit strip.text can specified separately. Facet strips dedicated position-dependent theme elements (strip.text.x.top, strip.text.x.bottom, strip.text.y.left, strip.text.y.right) inherit strip.text.x strip.text.y, respectively. consequence, theme stylings need applied position-dependent elements rather parent elements strip.switch.pad.grid space strips axes strips switched (unit) strip.switch.pad.wrap space strips axes strips switched (unit) complete set TRUE complete theme, one returned theme_grey(). Complete themes behave differently added ggplot object. Also, setting complete = TRUE elements set inherit blank elements. validate TRUE run validate_element(), FALSE bypass checks.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_theme.html","id":"theme-inheritance","dir":"Reference","previous_headings":"","what":"Theme inheritance","title":"Plot default theme — scheme_theme","text":"Theme elements inherit properties theme elements hierarchically. example, axis.title.x.bottom inherits axis.title.x inherits axis.title, turn inherits text. text elements inherit directly indirectly text; lines inherit line, rectangular objects inherit rect. means can modify appearance multiple elements setting single high-level component. Learn setting aesthetics vignette(\"ggplot2-specs\").","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_theme.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot default theme — scheme_theme","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 8) ggheatmap(small_mat) + scheme_theme(plot.background = element_rect(fill = \"red\")) #> → heatmap built with `geom_tile()` # `scheme_theme()` serves as the default theme and will always be # overridden by any `theme()` settings applied directly to the plot ggheatmap(small_mat) + theme(plot.background = element_rect(fill = \"blue\")) + scheme_theme(plot.background = element_rect(fill = \"red\")) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-LayoutProto-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Print Layout object — show,LayoutProto-method","title":"Print Layout object — show,LayoutProto-method","text":"Print Layout object","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-LayoutProto-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print Layout object — show,LayoutProto-method","text":"","code":"# S4 method for class 'LayoutProto' show(object)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-LayoutProto-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print Layout object — show,LayoutProto-method","text":"object quad_layout()/ggheatmap() stack_layout() object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-LayoutProto-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print Layout object — show,LayoutProto-method","text":"input invisiblely.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-ggalign_plot-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Show ggalign_plot information — show,ggalign_plot-method","title":"Show ggalign_plot information — show,ggalign_plot-method","text":"Show ggalign_plot information","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-ggalign_plot-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show ggalign_plot information — show,ggalign_plot-method","text":"","code":"# S4 method for class 'ggalign_plot' show(object)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-ggalign_plot-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show ggalign_plot information — show,ggalign_plot-method","text":"object ggalign_plot object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-ggalign_plot-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show ggalign_plot information — show,ggalign_plot-method","text":"input invisiblely.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_cross.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange plots crosswise horizontally or vertically — stack_cross","title":"Arrange plots crosswise horizontally or vertically — stack_cross","text":"stack_cross function derived stack_discrete() allows different layout ordering indices within single layout. Two aliases provided convenience: stack_crossv: special case stack_cross sets direction = \"v\" vertical alignment. stack_crossh: special case stack_cross sets direction = \"h\" horizontal alignment.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_cross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange plots crosswise horizontally or vertically — stack_cross","text":"","code":"stack_cross(direction, data = NULL, ..., theme = NULL, sizes = NA) stack_crossv(data = NULL, ...) stack_crossh(data = NULL, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_cross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange plots crosswise horizontally or vertically — stack_cross","text":"direction string indicating direction stack layout, either \"h\"(horizontal) \"v\"(vertical). data Default dataset use layout. specified, must supplied plot added layout, fortify_matrix() used convert data matrix. ... Additional arguments passed fortify_matrix(). theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. sizes numeric value unit object. used quad_layout() annotation, must length 1. used stack_layout() nested quad_layout(), length 3, specifying relative heights (direction = \"h\") widths (direction = \"v\") applied layout.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange plots horizontally or vertically — stack_layout","title":"Arrange plots horizontally or vertically — stack_layout","text":"limits provided, continuous variable required aligned direction specified (stack_continuous). Otherwise, discrete variable required aligned (stack_discrete). Several aliases provided convenience: stack_vertical: special case stack_layout sets direction = \"v\". stack_horizontal: special case stack_layout sets direction = \"h\". stack_discretev: special case stack_discrete sets direction = \"v\". stack_discreteh: special case stack_discrete sets direction = \"h\". stack_continuousv(): special case stack_free sets direction = \"v\". stack_continuoush(): special case stack_free sets direction = \"h\". historical reasons, following aliases available: stack_align alias stack_discrete. stack_alignv alias stack_discretev. stack_alignh alias stack_discreteh. stack_free alias stack_continuous. stack_freev alias stack_continuousv. stack_freeh alias stack_continuoush.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange plots horizontally or vertically — stack_layout","text":"","code":"stack_layout( direction, data = NULL, ..., theme = NULL, sizes = NA, limits = waiver() ) stack_horizontal(data = NULL, ..., limits = waiver()) stack_vertical(data = NULL, ..., limits = waiver()) stack_discrete(direction, data = NULL, ..., theme = NULL, sizes = NA) stack_discretev(data = NULL, ...) stack_discreteh(data = NULL, ...) stack_continuous( direction, data = NULL, ..., limits = NULL, theme = NULL, sizes = NA ) stack_continuousv(data = NULL, ...) stack_continuoush(data = NULL, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange plots horizontally or vertically — stack_layout","text":"direction string indicating direction stack layout, either \"h\"(horizontal) \"v\"(vertical). data Default dataset use layout. specified, must supplied plot added layout: limits provided, fortify_matrix() used get matrix. limits specified, fortify_data_frame() used get data frame. Note data matrix, automatically converted long-formatted data frame, differs ggplot2's behavior. ... Additional arguments passed fortify_data_frame() fortify_matrix(). theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. sizes numeric value unit object. used quad_layout() annotation, must length 1. used stack_layout() nested quad_layout(), length 3, specifying relative heights (direction = \"h\") widths (direction = \"v\") applied layout. limits continuous_limits() object specifying left/lower limit right/upper limit scale. Used align continuous axis.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange plots horizontally or vertically — stack_layout","text":"StackLayout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange plots horizontally or vertically — stack_layout","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7L) stack_horizontal(small_mat) + align_dendro() # this is the same with: stack_discrete(\"h\", small_mat) + align_dendro() stack_discreteh(small_mat) + align_dendro() # For vertical layout: stack_vertical(small_mat) + align_dendro()"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_switch.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine the active context of stack layout — stack_switch","title":"Determine the active context of stack layout — stack_switch","text":"stack_active alias stack_switch(), sets = NULL default.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_switch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the active context of stack layout — stack_switch","text":"","code":"stack_switch(sizes = NULL, what = waiver(), ...) stack_active(sizes = NULL, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_switch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the active context of stack layout — stack_switch","text":"sizes numeric value unit object. used quad_layout() annotation, must length 1. used stack_layout() nested quad_layout(), length 3, specifying relative heights (direction = \"h\") widths (direction = \"v\") applied layout. get activated stack layout? single number string plot elements layout. NULL, remove active context, useful active context quad_layout() object, align_*() added quad_layout(). removing active context, can add align_*() stack_layout(). ... dots future extensions must empty.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_switch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the active context of stack layout — stack_switch","text":"stack_switch object can added stack_layout().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_switch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine the active context of stack layout — stack_switch","text":"","code":"stack_discrete(\"h\", matrix(1:9, nrow = 3L)) + ggheatmap() + # ggheamtap will set the active context, directing following addition # into the heatmap plot area. To remove the heatmap active context, # we can use `stack_active()` which will direct subsequent addition into # the stack stack_active() + # here we add a dendrogram to the stack. align_dendro() #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/theme_no_axes.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove axis elements — theme_no_axes","title":"Remove axis elements — theme_no_axes","text":"Remove axis elements","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/theme_no_axes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove axis elements — theme_no_axes","text":"","code":"theme_no_axes( axes = \"xy\", text = TRUE, ticks = TRUE, title = TRUE, line = FALSE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/theme_no_axes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove axis elements — theme_no_axes","text":"axes axes elements removed? string containing one \"t\", \"l\", \"b\", \"r\", \"x\", \"y\". text TRUE, remove axis labels. ticks TRUE, remove axis ticks. title TRUE, remove axis title. line TRUE, remove axis line.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/theme_no_axes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove axis elements — theme_no_axes","text":"theme() object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/theme_no_axes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove axis elements — theme_no_axes","text":"","code":"p <- ggplot() + geom_point(aes(x = wt, y = qsec), data = mtcars) p + theme_no_axes() p + theme_no_axes(\"b\") p + theme_no_axes(\"l\")"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.MAF.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert the shape of a MAF for fortify method — tune.MAF","title":"Convert the shape of a MAF for fortify method — tune.MAF","text":"Convert shape MAF fortify method","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.MAF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert the shape of a MAF for fortify method — tune.MAF","text":"","code":"# S3 method for class 'MAF' tune(data, shape = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.MAF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert the shape of a MAF for fortify method — tune.MAF","text":"data MAF object. shape used currently.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.html","id":null,"dir":"Reference","previous_headings":"","what":"Change the shape of the input object — tune","title":"Change the shape of the input object — tune","text":"Change shape input object","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change the shape of the input object — tune","text":"","code":"tune(data, shape = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change the shape of the input object — tune","text":"data R object. shape Usually NULL string, specifying new shape object. Refer detailed method allowed values.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Change the shape of the input object — tune","text":"cases, fortify_matrix() fortify_data_frame() provide full support transforming objects. However, objects may require two completely different approaches fortified. tune function acts helper create new class tailored objects.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.list.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert the shape of a list for fortify method — tune.list","title":"Convert the shape of a list for fortify method — tune.list","text":"Convert shape list fortify method","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert the shape of a list for fortify method — tune.list","text":"","code":"# S3 method for class 'list' tune(data, shape = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert the shape of a list for fortify method — tune.list","text":"data list shape used currently.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert the shape of a matrix for fortify method — tune.matrix","title":"Convert the shape of a matrix for fortify method — tune.matrix","text":"Convert shape matrix fortify method","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert the shape of a matrix for fortify method — tune.matrix","text":"","code":"# S3 method for class 'matrix' tune(data, shape = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert the shape of a matrix for fortify method — tune.matrix","text":"data matrix. shape used currently.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify operated Context in quad_layout() — with_quad","title":"Modify operated Context in quad_layout() — with_quad","text":"with_quad() function modifies application context elements ggheatmap()/quad_layout(). controls objects like themes, scales, plot modifications apply specific annotation stacks main plot without altering currently active layout plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify operated Context in quad_layout() — with_quad","text":"","code":"with_quad(x, position = waiver(), main = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify operated Context in quad_layout() — with_quad","text":"x object can added ggplot, including schemes. See scheme_align(), scheme_data(), scheme_theme() position string specifying one positions- \"t\", \"l\", \"b\", \"r\"- indicate annotation stack context x. NULL, change operated context quad_layout() . default behaivours, see details section. main single boolean value indicating whether x apply main plot, used position NULL. default, position waiver() active context quad_layout() annotation stack active context stack_layout() , main set TRUE; otherwise, defaults FALSE.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify operated Context in quad_layout() — with_quad","text":"original object added attribute sets specified context.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Modify operated Context in quad_layout() — with_quad","text":"Default Behavior adding object wrapped with_quad(): quad_layout() object: ggheatmap()/quad_layout() active annotation stack, objects added via + - operate normally without with_quad(). active annotation stack set, with_quad() ensures applied object also modifies: main plot (default). Opposite annotation stacks using -. stack_layout() object: active layout stack_layout() : - operator apply changes plots along stack_layout(), means stack layout horizontal, - operator also add element left right annotation, stack layout vertical, - operator also add element top bottom annotation. + operator anything special. active layout nested ggheatmap()/quad_layout(), +/- operator applies elements nested layout, following principles ggheatmap()/quad_layout().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify operated Context in quad_layout() — with_quad","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) # By wrapping object with `with_quad()`, the `+` operator will apply the # object not only to the active plot in the annotation stack, but also to # the main plot unless specified by `main` argument otherwise. ggheatmap(small_mat) + # initialize the left annotation anno_left(size = 0.2) + align_dendro() + # apply the object not only to the active plot in the annotation stack, # but also to the main plot with_quad(theme(plot.background = element_rect(fill = \"red\"))) #> → heatmap built with `geom_tile()` # the `-` operator will apply changes not only to the active annotation # stack but also to the opposite one (i.e., bottom if top is active, and # vice versa). The same principle applies to the left and right annotation. ggheatmap(small_mat) + anno_left(size = 0.2) + align_dendro(aes(color = branch), k = 3L) + # Change the active layout to the left annotation anno_top(size = 0.2) + align_dendro(aes(color = branch), k = 3L) + anno_bottom(size = 0.2) + align_dendro(aes(color = branch), k = 3L) - # Modify the color scale of all plots in the bottom and the opposite # annotation, in this way, the `main` argument by default would be `TRUE` with_quad(scale_color_brewer(palette = \"Dark2\", name = \"Top and bottom\")) #> → heatmap built with `geom_tile()` # When the `position` argument is manually set, the # default value of the `main` argument will be `FALSE`. ggheatmap(small_mat) + anno_left(size = 0.2) + align_dendro(aes(color = branch), k = 3L) + anno_top(size = 0.2) + align_dendro(aes(color = branch), k = 3L) + anno_bottom(size = 0.2) + align_dendro(aes(color = branch), k = 3L) - # Modify the background of all plots in the left and top annotation with_quad(theme(plot.background = element_rect(fill = \"red\")), \"tl\") #> → heatmap built with `geom_tile()`"},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"breaking-changes-development-version","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"ggalign (development version)","text":"Now, *_free() layouts removed, layout splitted two type: align discrete continous vairables.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"new-features-development-version","dir":"Changelog","previous_headings":"","what":"New features","title":"ggalign (development version)","text":"new helper function memo_order() reorder oncoplot samples. new geom_subrect() geom_subtile() subdivide rectangles shared borders grid. new cross_link function reset layout ordering index layout panel group, add plot connect selected observations. new cross_mark function reset layout ordering index layout panel group, add plot annotate observations. new pair_links() function create pairs observation groups. new mark_draw(), mark_line(), mark_tetragon() define links connect marked observations. new link_draw(), link_line(), link_tetragon() define links connect pair observations new ggmark() add plot annotate selected observations. new element_vec() functions apply function vectorized fields theme element object. new no_expansion() function remove scale expansion. new layout circle_layout() arrange plot circular. new raster_magick() function post-processing image raster magick package added. new fortify_matrix.GISTIC() method GISTIC object maftools package (#24). + operator now respect with_quad(). new ggalign_attr_set() ggalign_attr_get() basic operations attached attribute. new geom_draw() function draw ggplot2 layer customized draw function.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"bug-fixes-development-version","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"ggalign (development version)","text":"fix breaks labels work well discrete scale (#30, #32) fix wrong results fortify_matrix.MAF() method","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"improvements-development-version","dir":"Changelog","previous_headings":"","what":"Improvements","title":"ggalign (development version)","text":"Now, with_quad() wraps object list class with_quad. approach offers greater flexibility defining actions associated with_quad, allowing customizable behavior (#26, @Yunuuuu). Now, panel reordered initializing layout parameters, don’t need reorder panel drawing. free_gg, align new cross_link objects collapsed one class ggalign_plot","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"ggalign-005","dir":"Changelog","previous_headings":"","what":"ggalign 0.0.5","title":"ggalign 0.0.5","text":"CRAN release: 2024-11-14","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"breaking-changes-0-0-5","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"ggalign 0.0.5","text":"direction argument stack_layout()/ggstack() soft-deprecated now, user must provide manually. set_context, order, name arguments align_*() ggheatmap() soft-deprecated, advised use active argument. guides, free_guides, free_spaces, free_labs, plot_data arguments align_*() ggheatmap() deprecated, advised use scheme_align function instead. theme argument align_*() ggheatmap() deprecated, advised use plot_theme function. argument stack_active() soft-deprecated, user advised use stack_switch() change active plot . align_panel()/ggpanel() deprecated, user advised use ggalign(data = NULL) instead.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"new-features-0-0-5","dir":"Changelog","previous_headings":"","what":"New features","title":"ggalign 0.0.5","text":"new quad_layout() create layout allowing free alignment. new quad_alignv(), quad_alignh(), quad_free()/ggside(), quad_alignb() alias quad_layout(). stack_layout() now gains type argument control whether layout align observations. new ggoncoplot() function draw oncoprint. new ggfree() function add ggplot layout. new fortify_matrix() function convert objects matrix, add fortify_matrix() method MAF object. new fortify_data_frame() function convert objects data frame. now, special attribute ggalign can used pass additional informations across building process, new function ggalign_attr() can used extract data attribute. new plot_theme() function control default theme plot layout. new plot_data() function control data transformation plot layout. new scheme_align() function control specifications plot layout. new with_quad() function control - operator context. new quad_init() function initialize annotation self-provided data. new stack_switch() quad_switch() switch active plots stack_layout() quad_layout(). new anno_top(), anno_left(), anno_bottom() anno_right() alias add annotation quad_layout(). align_dendro() gain new argument cutree customize process tree cutting. reorder_dendrogram argument align_dendro() function now can accept function reorder tree. new layer_order() function change ggplot2 layer adding order. new theme_no_axes() function remove axis elements. new geom_pie() function draw pie charts.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"bug-fixes-0-0-5","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"ggalign 0.0.5","text":"fix bug apply free_border alignpatches object. fix bug provide function distance argument align_dendro() fix bug provide hclust dendrogram method argument align_dendro() fix bug coord_ggalign() discrete scale","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"improvements-0-0-5","dir":"Changelog","previous_headings":"","what":"Improvements","title":"ggalign 0.0.5","text":"merge function implemented vctrs performance large matrix (> 20000 cells), automatically use geom_raster() {data.table} now removed dependency","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"ggalign-004","dir":"Changelog","previous_headings":"","what":"ggalign 0.0.4","title":"ggalign 0.0.4","text":"CRAN release: 2024-10-12 layout_heatmap()/ggheatmap() arguments width/height renamed .width/.height helps avoid conflicts arguments geom_tile(). nestet alignpatches theme default inherit parent alignpatches new layout_title() function, now layout_annotation() control layout theme add ggrastr::rasterize method ggheatmap() ggstack() set_context argument align_dendro() now depends plot_dendrogram default align_dendro() gain new argument reorder_dendrogram control whether reorder generated dendrogram based mean values. align_reorder() now splitted two function align_order() align_reorder() dendrogram_data() gain new argument reorder_branches control whether reorder input leaf_braches based tree. align_dendro() gain new argument merge_dendrogram control whether dendrograms multiple groups merged dendrogram height axis automatically reversed bottom left annotation stack heatmap fill color scale now default use scale_fill_gradient2(low = \"blue\", high = \"red\") continuous values. Coord used set limits instead Scale free_* arguments now accept argument corresponding free_* functions. new theme_ggalign() function default theme ggalign package export option ggalign.default_theme allow user change global default theme new free_guide() function, override layout guides argument single plot geom_draw() now utilize patch() function convert objects grob internal changes: vectors operated vctrs package stack_layout(): gain sizes argument control relative sizes stack align_()*: now order argument control plot area. align_reorder() now can accept ordering character names. export order2() function align_reorder(): fun argument renamed order argument, can now accept ordering integer index directly fun align_reorder() now can return statistics can handled order2() fix ggheatmap() order work put stack layout method hclust2() can now return objects can coerced hclust, can provide object directly method. hclust2() now can accept distance = NULL hmanno(), stack_active(), align_*() functions gain new argument theme control theme plot. new layout_annotation() layout_theme() modify layout components borders argument free_space() renamed spaces {tibble} now removed dependency align_plots() now can accept gList, function, recordedplot, trellis, pheatmap, Heatmap, HeatmapAnnotation, HeatmapList, added alignpatch method objects. add patch method gList, function, recordedplot, trellis, pheatmap, Heatmap, HeatmapAnnotation, HeatmapList fix bug wrap() function duplicated names gtable cause grobs missing new free_vp() function customize viewport aligning. StackLayout HeatmapLayout methods collapsed one method Layout class New Patch class, now can extend alignment process object customize building process ggproto. fix missing variable labs free_space method PatchAlignpatches","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"ggalign-003","dir":"Changelog","previous_headings":"","what":"ggalign 0.0.3","title":"ggalign 0.0.3","text":"CRAN release: 2024-09-15 Add package logo new inset() function add package quotes DESCRIPTION add return value docs exported function methods","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"ggalign-002","dir":"Changelog","previous_headings":"","what":"ggalign 0.0.2","title":"ggalign 0.0.2","text":"omit redudnant description add single quote package name","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"features-0-0-1","dir":"Changelog","previous_headings":"","what":"Features","title":"ggalign 0.0.1","text":"ggalign pacakge provides two layout arrange ggplot objects: heatmap_layout()/ggheatmap(): Arrange ggplot Heatmap layout. See vignette(\"heatmap-layout\") details. stack_layout()/ggstack(): Arrange ggplot vertically horizontally. See vignette(\"stack-layout\") details. customize layouts, offer following functions: align_group(): Group layout axis panel group variable. align_kmeans(): Group layout axis panel kmeans align_reorder(): Reorders layout observations based weights summary statistics. align_dendro(): Reorder Group layout based hierarchical clustering detailed instructions customizing layouts, see vignette: vignette(\"layout-customize\"). Additionally, plots can added layout following functions: align_gg()/ggalign(): Create ggplot object customized data. align_panel()/ggpanel(): Create ggplot object layout panel data. information adding plots, refer vignette: vignette(\"layout-plot\").","code":""}] +[{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement yunyunp96@163.com. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 ggalign authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/articles/FAQ.html","id":"can-i-change-the-default-data-for-all-geoms","dir":"Articles","previous_headings":"","what":"Can I change the default data for all geoms?","title":"FAQ","text":"function ggalign requires specific data formats operations. need transform filter data individual geoms, can use data argument within geom. However, multiple geoms want consistent transformation applied across , can utilize scheme_data() function allows transform default data additive geoms.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/articles/FAQ.html","id":"why-are-there-spaces-after-setting-all-plot-margin-to-zero","dir":"Articles","previous_headings":"","what":"Why are there spaces after setting all plot.margin to zero?","title":"FAQ","text":"default, ggalign doesn’t add spaces plots. notice spaces, likely due : Plot margins within individual plots. Scale expansion automatically added ggplot2. can resolve removing scale expansion adjusting margins theme:","code":"ggheatmap(small_mat) + anno_top() + align_dendro(aes(color = branch), k = 3L) + scale_y_continuous(expand = expansion()) & theme(plot.margin = margin()) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/articles/FAQ.html","id":"why-cant-i-add-two-dendrograms-with-different-reorder-settings","dir":"Articles","previous_headings":"","what":"Why can’t I add two dendrograms with different reorder settings?","title":"FAQ","text":"Note: always prevent users reordering layout direction twice. reorder_group = FALSE used, reordering heatmap occurs within group. long ordering within group remains consistent, two dendrograms can placed axis heatmap. Let’s assume panels represents group observation index represents ordered index observations. code provided, panels initialized ungrouped index unordered: add dendrogram reorder_group = FALSE; ’ll something like (Since reorder_group = FALSE, panels won’t changed): However, dendrogram reorder_group = TRUE added, reorder panels, underlying index changed: prevent reordering axis twice, ensure new_index matches index (index NULL). done maintain consistency prevent conflicts ordering heatmap.","code":"panels <- NULL index <- NULL set.seed(2L) group <- sample(letters[1:3], ncol(small_mat), replace = TRUE) h <- ggheatmap(small_mat) + anno_top() + align_group(group) h1 <- h + align_dendro(reorder_group = FALSE, merge_dendrogram = TRUE) # always remember dendrogram will initialize the index, here, we extract the # index from the underlying dendrogram index <- stats::order.dendrogram(ggalign_stat(h1, \"top\", 2L)) h2 <- h + align_dendro(reorder_group = TRUE, merge_dendrogram = TRUE) new_index <- stats::order.dendrogram(ggalign_stat(h2, \"top\", 2L)) all(index == new_index) #> [1] FALSE"},{"path":"https://yunuuuu.github.io/ggalign/dev/articles/FAQ.html","id":"session-information","dir":"Articles","previous_headings":"","what":"Session information","title":"FAQ","text":"","code":"sessionInfo() #> R version 4.4.2 (2024-10-31) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 24.04.1 LTS #> #> Matrix products: default #> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0 #> #> locale: #> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 #> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 #> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C #> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C #> #> time zone: UTC #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] ggalign_0.0.5.9000 ggplot2_3.5.1 #> #> loaded via a namespace (and not attached): #> [1] vctrs_0.6.5 cli_3.6.3 knitr_1.49 rlang_1.1.5 #> [5] xfun_0.50 generics_0.1.3 textshaping_0.4.1 jsonlite_1.8.9 #> [9] labeling_0.4.3 glue_1.8.0 colorspace_2.1-1 htmltools_0.5.8.1 #> [13] ragg_1.3.3 sass_0.4.9 scales_1.3.0 rmarkdown_2.29 #> [17] grid_4.4.2 tibble_3.2.1 evaluate_1.0.3 munsell_0.5.1 #> [21] jquerylib_0.1.4 fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4 #> [25] compiler_4.4.2 dplyr_1.1.4 fs_1.6.5 pkgconfig_2.0.3 #> [29] farver_2.1.2 systemfonts_1.2.0 digest_0.6.37 R6_2.5.1 #> [33] tidyselect_1.2.1 pillar_1.10.1 magrittr_2.0.3 bslib_0.8.0 #> [37] withr_3.0.2 tools_4.4.2 gtable_0.3.6 pkgdown_2.1.1 #> [41] cachem_1.1.0 desc_1.4.3"},{"path":"https://yunuuuu.github.io/ggalign/dev/articles/benchmarks.html","id":"compared-with-other-packages","dir":"Articles","previous_headings":"","what":"Compared with other packages","title":"Benchmarks","text":"simple heatmap. heatmap dendrogram","code":"bench::mark( \"heatmap()\" = { pdf(NULL) heatmap(mat, Rowv = NA, Colv = NA) dev.off() NULL }, \"heatmap.2()\" = { pdf(NULL) heatmap.2(mat, dendrogram = \"none\", trace = \"none\") dev.off() NULL }, \"Heatmap()\" = { pdf(NULL) draw(Heatmap(mat, cluster_rows = FALSE, cluster_columns = FALSE, use_raster = TRUE )) dev.off() NULL }, \"pheatmap()\" = { pdf(NULL) pheatmap(mat, cluster_rows = FALSE, cluster_cols = FALSE) dev.off() NULL }, \"ggalign()\" = { pdf(NULL) print(ggheatmap(mat, filling = \"raster\")) dev.off() NULL } ) #> Warning: Some expressions had a GC in every iteration; so filtering is #> disabled. #> # A tibble: 5 × 6 #> expression min median `itr/sec` mem_alloc `gc/sec` #> #> 1 heatmap() 144.09ms 146.62ms 6.59 139.11MB 3.30 #> 2 heatmap.2() 2.26s 2.26s 0.443 224.23MB 0.886 #> 3 Heatmap() 4.36s 4.36s 0.229 792.59MB 2.98 #> 4 pheatmap() 663.6ms 663.6ms 1.51 124.1MB 3.01 #> 5 ggalign() 2.4s 2.4s 0.416 2.51GB 10.4 bench::mark( \"heatmap()\" = { pdf(NULL) heatmap(mat) dev.off() NULL }, \"heatmap.2()\" = { pdf(NULL) heatmap.2(mat, trace = \"none\") dev.off() NULL }, \"Heatmap()\" = { pdf(NULL) draw(Heatmap(mat, row_dend_reorder = FALSE, column_dend_reorder = FALSE, use_raster = TRUE )) dev.off() NULL }, \"pheatmap()\" = { pdf(NULL) pheatmap(mat) dev.off() NULL }, \"ggalign()\" = { pdf(NULL) print(ggheatmap(mat, filling = \"raster\") + anno_top() + align_dendro() + anno_right() + align_dendro()) dev.off() NULL } ) #> Warning: Some expressions had a GC in every iteration; so filtering is #> disabled. #> # A tibble: 5 × 6 #> expression min median `itr/sec` mem_alloc `gc/sec` #> #> 1 heatmap() 2.64s 2.64s 0.378 173.72MB 2.65 #> 2 heatmap.2() 2.78s 2.78s 0.359 223.41MB 2.52 #> 3 Heatmap() 5.9s 5.9s 0.169 1.51GB 2.37 #> 4 pheatmap() 2.26s 2.26s 0.443 177.53MB 0.443 #> 5 ggalign() 5.11s 5.11s 0.196 2.58GB 5.29"},{"path":"https://yunuuuu.github.io/ggalign/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Yun Peng. Author, maintainer. Shixiang Wang. Author.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Peng Y, Wang S (2025). ggalign: 'ggplot2' Extension Consistent Axis Alignment. R package version 0.0.5.9000, https://yunuuuu.github.io/ggalign/, https://github.com/Yunuuuu/ggalign.","code":"@Manual{, title = {ggalign: A 'ggplot2' Extension for Consistent Axis Alignment}, author = {Yun Peng and Shixiang Wang}, year = {2025}, note = {R package version 0.0.5.9000, https://yunuuuu.github.io/ggalign/}, url = {https://github.com/Yunuuuu/ggalign}, }"},{"path":"https://yunuuuu.github.io/ggalign/dev/index.html","id":"ggalign-","dir":"","previous_headings":"","what":"A ggplot2 Extension for Consistent Axis Alignment","title":"A ggplot2 Extension for Consistent Axis Alignment","text":"package extends ggplot2 providing advanced tools aligning organizing multiple plots, particularly automatically reorder observations, dendrogram. offers fine control layout adjustment plot annotations, enabling create complex, publication-quality visualizations still using familiar grammar ggplot2.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/index.html","id":"why-use-ggalign","dir":"","previous_headings":"","what":"Why use ggalign?","title":"A ggplot2 Extension for Consistent Axis Alignment","text":"ggalign focuses aligning observations across multiple plots. leverages \"number observations\" vctrs package NROW() function maintain consistency plot organization. ’ve ever struggled aligning plots self-contained ordering (like dendrogram), applying consistent grouping ordering across multiple plots (e.g., k-means clustering), ggalign designed make easier. package integrates seamlessly ggplot2, providing flexibility use geoms, scales, components complex visualizations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"A ggplot2 Extension for Consistent Axis Alignment","text":"can install ggalign CRAN using: Alternatively, install development version r-universe : GitHub :","code":"install.packages(\"ggalign\") install.packages(\"ggalign\", repos = c(\"https://yunuuuu.r-universe.dev\", \"https://cloud.r-project.org\") ) # install.packages(\"remotes\") remotes::install_github(\"Yunuuuu/ggalign\")"},{"path":"https://yunuuuu.github.io/ggalign/dev/index.html","id":"learning-ggalign","dir":"","previous_headings":"","what":"Learning ggalign","title":"A ggplot2 Extension for Consistent Axis Alignment","text":"complete tutorial available : https://yunuuuu.github.io/ggalign-book/ full reference documentation, visit: https://yunuuuu.github.io/ggalign/","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/index.html","id":"acknowledgements","dir":"","previous_headings":"","what":"Acknowledgements","title":"A ggplot2 Extension for Consistent Axis Alignment","text":"like express sincere gratitude contributors ggplot2 project providing powerful flexible framework data visualization R. work laid foundation functionality design package. also like thank patchwork project, core coding plot composer adapted. patchwork library provided useful mechanism combining aligning plots, modified suit needs package. Without contributions open-source projects, package possible. Additionally, like extend heartfelt thanks @teunbrand, fulfilled numerous feature requests, assisted integration new functions ggplot2.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/LayoutProto-class.html","id":null,"dir":"Reference","previous_headings":"","what":"A Layout object — LayoutProto-class","title":"A Layout object — LayoutProto-class","text":"Layout object defines place plots.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/active.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Adding Context Settings — active","title":"Plot Adding Context Settings — active","text":"settings control behavior plot added layout, well arrangement individual plot areas within layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/active.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Adding Context Settings — active","text":"","code":"active(order = waiver(), use = waiver(), name = waiver())"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/active.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Adding Context Settings — active","text":"order integer specifying order plot area within layout. use logical (TRUE/FALSE) indicating whether set active context current plot added layout. TRUE, subsequent ggplot elements applied plot. name string specifying plot's name, useful switching active contexts argument functions like quad_anno()/stack_switch().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/active.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot Adding Context Settings — active","text":"default, active context set functions add plot areas. allows ggplot2 elements-geoms, stats, scales, themes- seamlessly added current plot area. default ordering plot areas top bottom left right, depending layout orientation. However, users can customize order using order argument.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a New align Object — align","title":"Create a New align Object — align","text":"Align object interacts Layout object reorder split observations , cases, add plot components Layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a New align Object — align","text":"","code":"align( align, data = NULL, ..., plot = NULL, size = NULL, schemes = NULL, no_axes = NULL, active = NULL, call = caller_call() )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a New align Object — align","text":"align Align object. data following options can used: NULL: data set. waiver(): Inherits data layout matrix. function (including purrr-like lambda syntax): Applied layout matrix transform data use. transform final plot data, please use scheme_data(). matrix, data.frame, atomic vector. ... Additional fields passed align object. plot ggplot object. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. schemes Options schemes: NULL: Used align add plot. waiver(): Try infer schemes based data. no_axes Logical; TRUE, removes axes elements alignment axis using theme_no_axes(). default, use option- \"ggalign.align_no_axes\". active active() object defines context settings added layout. call call used construct Align object, reporting messages.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a New align Object — align","text":"new ggalign_plot object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a New align Object — align","text":"Align* objects just ggproto() object, descended top-level Align, implements various methods fields. create new type Align* object, typically want override one following: setup_params: Prepare parameter check parameters used plot. setup_data: Prepare data used plot. compute: method used compute statistics. align: method used group observations panel reorder observations. draw: method used draw plot. Must return ggplot object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Create a New align Object — align","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a New align Object — align","text":"","code":"align_dendro() #> #> plot: yes #> reorder: yes #> split: no"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot dendrogram tree — align_dendro","title":"Plot dendrogram tree — align_dendro","text":"Plot dendrogram tree","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot dendrogram tree — align_dendro","text":"","code":"align_dendro( mapping = aes(), ..., distance = \"euclidean\", method = \"complete\", use_missing = \"pairwise.complete.obs\", reorder_dendrogram = FALSE, merge_dendrogram = FALSE, reorder_group = FALSE, k = NULL, h = NULL, cutree = NULL, plot_dendrogram = TRUE, plot_cut_height = NULL, root = NULL, center = FALSE, type = \"rectangle\", size = NULL, data = NULL, no_axes = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot dendrogram tree — align_dendro","text":"mapping Default list aesthetic mappings use plot. specified, must supplied layer added plot. ... Additional arguments passed geom_segment(). distance string distance measure used. must one \"euclidean\", \"maximum\", \"manhattan\", \"canberra\", \"binary\" \"minkowski\". Correlation coefficient can also used, including \"pearson\", \"spearman\" \"kendall\". way, 1 - cor used distance. addition, can also provide dist object directly function return dist object. Use NULL, want calculate distance. method string agglomeration method used. (unambiguous abbreviation ) one \"ward.D\", \"ward.D2\", \"single\", \"complete\", \"average\" (= UPGMA), \"mcquitty\" (= WPGMA), \"median\" (= WPGMC) \"centroid\" (= UPGMC). can also provide function accepts calculated distance (input matrix distance NULL) returns hclust object. Alternative, can supply object can coerced hclust. use_missing optional character string giving method computing covariances presence missing values. must (abbreviation ) one strings \"everything\", \".obs\", \"complete.obs\", \"na..complete\", \"pairwise.complete.obs\". used distance correlation coefficient string. reorder_dendrogram single boolean value indicating whether reorder dendrogram based means. Alternatively, can provide custom function accepts hclust object data used generate tree, returning either hclust dendrogram object. Default FALSE. merge_dendrogram single boolean value, indicates whether merge multiple dendrograms, used previous groups established. Default: FALSE. reorder_group single boolean value, indicates whether Hierarchical Clustering groups, used previous groups established. Default: FALSE. k integer scalar indicates desired number groups. h numeric scalar indicates heights tree cut. cutree function used cut hclust tree. accept four arguments: hclust tree object, distance (applicable method string function performing hierarchical clustering), k (number clusters), h (height cut tree). default, cutree() used. plot_dendrogram boolean value indicates whether plot dendrogram tree. plot_cut_height boolean value indicates whether plot cut height. root length one string numeric indicates root branch. center boolean value. TRUE, nodes plotted centered respect leaves/tips branch. Otherwise (default), plot middle direct child nodes. type string indicates plot type, \"rectangle\" \"triangle\". size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. data matrix-like object. default, inherits layout matrix. no_axes Logical; TRUE, removes axes elements alignment axis using theme_no_axes(). default, use option- \"ggalign.align_no_axes\". active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Plot dendrogram tree — align_dendro","text":"align_dendro initializes ggplot data mapping. internal ggplot object always use default mapping aes(x = .data$x, y = .data$y). default ggplot data node coordinates edge data attached ggalign attribute, addition, geom_segment layer data frame edge coordinates added plot_dendrogram = TRUE. See fortify_data_frame.dendrogram() details.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Plot dendrogram tree — align_dendro","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_dendro.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot dendrogram tree — align_dendro","text":"","code":"# align_dendro will always add a plot area ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + align_dendro() #> → heatmap built with `geom_tile()` ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + align_dendro(k = 3L) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_group.html","id":null,"dir":"Reference","previous_headings":"","what":"Group and align observations based on a group vector — align_group","title":"Group and align observations based on a group vector — align_group","text":"Splits observations groups, slice ordering based group levels.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_group.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Group and align observations based on a group vector — align_group","text":"","code":"align_group(group, active = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_group.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Group and align observations based on a group vector — align_group","text":"group character define groups observations. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_group.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Group and align observations based on a group vector — align_group","text":"","code":"set.seed(1L) small_mat <- matrix(rnorm(81), nrow = 9) ggheatmap(small_mat) + anno_top() + align_group(sample(letters[1:4], ncol(small_mat), replace = TRUE)) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_hclust.html","id":null,"dir":"Reference","previous_headings":"","what":"Reorder or Group observations based on hierarchical clustering — align_hclust","title":"Reorder or Group observations based on hierarchical clustering — align_hclust","text":"function aligns observations within layout according hierarchical clustering tree, enabling reordering grouping elements based clustering results.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_hclust.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reorder or Group observations based on hierarchical clustering — align_hclust","text":"","code":"align_hclust( distance = \"euclidean\", method = \"complete\", use_missing = \"pairwise.complete.obs\", reorder_dendrogram = FALSE, reorder_group = FALSE, k = NULL, h = NULL, cutree = NULL, data = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_hclust.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reorder or Group observations based on hierarchical clustering — align_hclust","text":"distance string distance measure used. must one \"euclidean\", \"maximum\", \"manhattan\", \"canberra\", \"binary\" \"minkowski\". Correlation coefficient can also used, including \"pearson\", \"spearman\" \"kendall\". way, 1 - cor used distance. addition, can also provide dist object directly function return dist object. Use NULL, want calculate distance. method string agglomeration method used. (unambiguous abbreviation ) one \"ward.D\", \"ward.D2\", \"single\", \"complete\", \"average\" (= UPGMA), \"mcquitty\" (= WPGMA), \"median\" (= WPGMC) \"centroid\" (= UPGMC). can also provide function accepts calculated distance (input matrix distance NULL) returns hclust object. Alternative, can supply object can coerced hclust. use_missing optional character string giving method computing covariances presence missing values. must (abbreviation ) one strings \"everything\", \".obs\", \"complete.obs\", \"na..complete\", \"pairwise.complete.obs\". used distance correlation coefficient string. reorder_dendrogram single boolean value indicating whether reorder dendrogram based means. Alternatively, can provide custom function accepts hclust object data used generate tree, returning either hclust dendrogram object. Default FALSE. reorder_group single boolean value, indicates whether Hierarchical Clustering groups, used previous groups established. Default: FALSE. k integer scalar indicates desired number groups. h numeric scalar indicates heights tree cut. cutree function used cut hclust tree. accept four arguments: hclust tree object, distance (applicable method string function performing hierarchical clustering), k (number clusters), h (height cut tree). default, cutree() used. data matrix-like object. default, inherits layout matrix. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_hclust.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Reorder or Group observations based on hierarchical clustering — align_hclust","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_hclust.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reorder or Group observations based on hierarchical clustering — align_hclust","text":"","code":"# align_hclust won't add a dendrogram ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + align_hclust(k = 3L) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_kmeans.html","id":null,"dir":"Reference","previous_headings":"","what":"Split observations by k-means clustering groups. — align_kmeans","title":"Split observations by k-means clustering groups. — align_kmeans","text":"Aligns groups observations based k-means clustering, enabling observation splits cluster groups.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_kmeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split observations by k-means clustering groups. — align_kmeans","text":"","code":"align_kmeans(..., data = NULL, active = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_kmeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split observations by k-means clustering groups. — align_kmeans","text":"... Arguments passed stats::kmeans iter.max maximum number iterations allowed. nstart centers number, many random sets chosen? algorithm character: may abbreviated. Note \"Lloyd\" \"Forgy\" alternative names one algorithm. trace logical integer number, currently used default method (\"Hartigan-Wong\"): positive (true), tracing information progress algorithm produced. Higher values may produce tracing information. data numeric matrix used k-means. default, inherit layout matrix. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_kmeans.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Split observations by k-means clustering groups. — align_kmeans","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_kmeans.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split observations by k-means clustering groups. — align_kmeans","text":"","code":"ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + align_kmeans(3L) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_order.html","id":null,"dir":"Reference","previous_headings":"","what":"Order observations based on weights — align_order","title":"Order observations based on weights — align_order","text":"Ordering observations based summary weights specified ordering character integer index.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_order.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Order observations based on weights — align_order","text":"","code":"align_order( weights = rowMeans, ..., reverse = FALSE, strict = TRUE, data = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_order.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Order observations based on weights — align_order","text":"weights summary function accepts data returns weights observations. Alternatively, can provide ordering index either integer character. Since characters designated character indices, wish specify function name string, must enclose (). ... Additional arguments passed function provided weights argument. reverse boolean value. sort order reverse? strict boolean value indicates whether order strict. previous groups established, strict FALSE, reorder observations group. data matrix, data frame, atomic vector used input weights function. Alternatively, can specify function (including purrr-like lambda syntax) applied layout matrix, transforming necessary weight calculations. default, inherit layout matrix. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_order.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Order observations based on weights — align_order","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_order.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Order observations based on weights — align_order","text":"","code":"ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_left() + align_order(I(\"rowMeans\")) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_panel.html","id":null,"dir":"Reference","previous_headings":"","what":"Create ggplot object with layout panel data — align_panel","title":"Create ggplot object with layout panel data — align_panel","text":"function deprecated realised special case ggalign() function. Please use ggalign(data = NULL) instead.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_panel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create ggplot object with layout panel data — align_panel","text":"","code":"align_panel(...) ggpanel(...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Phylogenetics tree — align_phylo","title":"Plot Phylogenetics tree — align_phylo","text":"Plot Phylogenetics tree","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Phylogenetics tree — align_phylo","text":"","code":"align_phylo( phylo, ..., ladderize = NULL, type = \"rectangle\", center = FALSE, tree_type = NULL, no_axes = NULL, active = NULL, size = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Phylogenetics tree — align_phylo","text":"phylo phylo object. ... Additional arguments passed geom_segment(). ladderize single string \"left\" \"right\", indicating whether ladderize tree. Ladderizing arranges tree smallest clade positioned \"right\" \"left\". default, NULL means tree ladderized. type string indicates plot type, \"rectangle\" \"triangle\". center boolean value. TRUE, nodes plotted centered respect leaves/tips branch. Otherwise (default), plot middle direct child nodes. tree_type single string, one \"phylogram\" \"cladogram\", indicating type tree. phylogram: Represents phylogenetic tree branch lengths indicate evolutionary distance time. cladogram: Represents tree branch lengths used, branches reflect evolutionary time. Usually, need modify . no_axes Logical; TRUE, removes axes elements alignment axis using theme_no_axes(). default, use option- \"ggalign.align_no_axes\". active active() object defines context settings added layout. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange multiple plots into a grid — align_plots","title":"Arrange multiple plots into a grid — align_plots","text":"Arrange multiple plots grid","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange multiple plots into a grid — align_plots","text":"","code":"align_plots( ..., ncol = NULL, nrow = NULL, byrow = TRUE, widths = NA, heights = NA, design = NULL, guides = waiver(), theme = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange multiple plots into a grid — align_plots","text":"... list plots, ususally ggplot object. Use NULL indicate empty spacer. ncol, nrow dimensions grid create - NULL use logic facet_wrap() set dimensions byrow FALSE plots filled column-major order. widths, heights relative widths heights column row grid. get repeated match dimensions grid. special value NA behave 1null unit unless fixed aspect plot inserted case allow dimension expand contract match aspect ratio content. design Specification location areas layout. Can either specified text string concatenating calls area() together. guides string one \"t\", \"l\", \"b\", \"r\" indicating side guide legends collected. Defaults waiver(), inherits parent layout. parent layout, NULL provided, guides collected. theme theme() object used customize various elements plot, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange multiple plots into a grid — align_plots","text":"alignpatches object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange multiple plots into a grid — align_plots","text":"","code":"# directly copied from patchwork p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p3 <- ggplot(mtcars) + geom_bar(aes(gear)) + facet_wrap(~cyl) p4 <- ggplot(mtcars) + geom_bar(aes(carb)) p5 <- ggplot(mtcars) + geom_violin(aes(cyl, mpg, group = cyl)) # Either add the plots as single arguments align_plots(p1, p2, p3, p4, p5) # Or use bang-bang-bang to add a list align_plots(!!!list(p1, p2, p3), p4, p5) # Match plots to areas by name design <- \"#BB AA#\" align_plots(B = p1, A = p2, design = design) # Compare to not using named plot arguments align_plots(p1, p2, design = design)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":null,"dir":"Reference","previous_headings":"","what":"Reorders layout observations based on specific statistics. — align_reorder","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"Reorders layout observations based specific statistics.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"","code":"align_reorder( stat, ..., reverse = FALSE, strict = TRUE, data = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"stat statistical function accepts data returns statistic, call order2() extract ordering information. ... Additional arguments passed function provided stat argument. reverse boolean value. sort order reverse? strict boolean value indicates whether order strict. previous groups established, strict FALSE, reorder observations group. data matrix, data frame, atomic vector used input stat function. Alternatively, can specify function (including purrr-like lambda syntax) applied layout matrix, transforming necessary statistic calculations. default, inherit layout matrix. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"align_reorder() function differs align_order() weights argument align_order() must return atomic weights observation. contrast, stat argument align_reorder() can return complex structures, hclust dendrogram, among others. Typically, can achieve functionality align_reorder() using align_order() manually extracting ordering information statistic.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/align_reorder.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reorders layout observations based on specific statistics. — align_reorder","text":"","code":"ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_left() + align_reorder(hclust2) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare plots to be aligned with align_plots — alignpatch","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"Prepare plots aligned align_plots","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"","code":"alignpatch(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"x plot object prepared alignment.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"Patch object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"ggalign implement alignpatch method following objects: ggplot alignpatches wrapped_plot patch wrapped_patch spacer","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/alignpatch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prepare plots to be aligned with align_plots — alignpatch","text":"","code":"alignpatch(ggplot()) #> #> add_background: function #> add_plot: function #> align_border: function #> align_free_border: function #> align_panel_sizes: function #> collect_guides: function #> free_border: function #> free_lab: function #> get_sizes: function #> patch_gtable: function #> plot: gg, ggplot #> respect: function #> set_guides: function #> set_theme: function #> split_gt: function #> super: "},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the plotting areas in align_plots — area","title":"Define the plotting areas in align_plots — area","text":"small helper used specify single area rectangular grid contain plot. Objects constructed area() can concatenated together c() order specify multiple areas.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the plotting areas in align_plots — area","text":"","code":"area(t, l, b = t, r = l)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the plotting areas in align_plots — area","text":"t, b top bottom bounds area grid l, r left right bounds area int grid","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define the plotting areas in align_plots — area","text":"ggalign_area object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Define the plotting areas in align_plots — area","text":"grid areas specified reference enumerate rows top bottom, coloumns left right. means t l always less equal b r respectively. Instead specifying area placement combination area() calls, possible instead pass single string equivalent ","code":"areas <- c(area(1, 1, 2, 1), area(2, 3, 3, 3)) areas < -\"A## A#B ##B\""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/area.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define the plotting areas in align_plots — area","text":"","code":"p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p3 <- ggplot(mtcars) + geom_bar(aes(gear)) + facet_wrap(~cyl) layout <- c( area(1, 1), area(1, 3, 3), area(3, 1, 3, 2) ) #> Error in vec_slice(vec_data(x), i): Can't use character names to index an unnamed vector. # Show the layout to make sure it looks as it should plot(layout) #> Error in curve(expr = x, from = from, to = to, xlim = xlim, ylab = ylab, ...): 'expr' did not evaluate to an object of length 'n' # Apply it to a alignpatches align_plots(p1, p2, p3, design = layout) #> Error in as_areas(design): Cannot convert a function into a design area"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cash-LayoutProto-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset a Layout object — $,LayoutProto-method","title":"Subset a Layout object — $,LayoutProto-method","text":"Used ggplot_build ggsave","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cash-LayoutProto-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset a Layout object — $,LayoutProto-method","text":"","code":"# S4 method for class 'LayoutProto' x$name"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cash-LayoutProto-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset a Layout object — $,LayoutProto-method","text":"x Layout object name string slot name Layout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cash-LayoutProto-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset a Layout object — $,LayoutProto-method","text":"slot value.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange plots in a circular layout — circle_layout","title":"Arrange plots in a circular layout — circle_layout","text":"limits provided, continuous variable required aligned direction specified (circle_continuous). Otherwise, discrete variable required aligned (circle_discrete).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange plots in a circular layout — circle_layout","text":"","code":"circle_layout( data = NULL, ..., radial = NULL, direction = \"outward\", limits = waiver(), theme = NULL ) circle_discrete( data = NULL, ..., radial = NULL, direction = \"outward\", theme = NULL ) circle_continuous( data = NULL, ..., radial = NULL, direction = \"outward\", limits = NULL, theme = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange plots in a circular layout — circle_layout","text":"data Default dataset use layout. specified, must supplied plot added layout: limits provided, fortify_matrix() used get matrix. limits specified, fortify_data_frame() used get data frame. Note data matrix, automatically converted long-formatted data frame, differs ggplot2's behavior. ... Additional arguments passed fortify_data_frame() fortify_matrix(). radial coord_radial() object defines global parameters coord_radial across plots layout. parameters start, end, direction, expand inherited applied uniformly plots within layout. parameters theta r.axis.inside always ignored set \"x\" TRUE, respectively, plots. direction single string \"inward\" \"outward\", indicating direction plot added. outward: plot added inner outer. inward: plot added outer inner. limits continuous_limits() object specifying left/lower limit right/upper limit scale. Used align continuous axis. theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange plots in a circular layout — circle_layout","text":"CircleLayout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange plots in a circular layout — circle_layout","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) rownames(small_mat) <- paste0(\"row\", seq_len(nrow(small_mat))) colnames(small_mat) <- paste0(\"column\", seq_len(ncol(small_mat))) # circle_layout # same for circle_discrete() circle_layout(small_mat) + ggalign() + geom_tile(aes(y = .column_index, fill = value)) + scale_fill_viridis_c() + align_dendro(aes(color = branch), k = 3L) + scale_color_brewer(palette = \"Dark2\") # same for circle_continuous() circle_layout(mpg, limits = continuous_limits(c(3, 5))) + ggalign(mapping = aes(displ, hwy, colour = class)) + geom_point(size = 2) + ggalign(mapping = aes(displ, hwy, colour = class)) + geom_point(size = 2) & scale_color_brewer(palette = \"Dark2\") & theme_bw() # circle_discrete() # direction outward circle_discrete(small_mat) + align_dendro(aes(color = branch), k = 3L) + scale_color_brewer(palette = \"Dark2\") + ggalign() + geom_tile(aes(y = .column_index, fill = value)) + scale_fill_viridis_c() # direction inward circle_discrete(small_mat, direction = \"inward\") + ggalign() + geom_tile(aes(y = .column_index, fill = value)) + scale_fill_viridis_c() + align_dendro(aes(color = branch), k = 3L) + scale_color_brewer(palette = \"Dark2\") # circle_continuous() circle_continuous(mpg, limits = continuous_limits(c(3, 5))) + ggalign(mapping = aes(displ, hwy, colour = class)) + geom_point(size = 2) + ggalign(mapping = aes(displ, hwy, colour = class)) + geom_point(size = 2) & scale_color_brewer(palette = \"Dark2\") & theme_bw()"},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_switch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the active context of circle layout — circle_switch","text":"","code":"circle_switch(radial = waiver(), direction = NULL, what = waiver(), ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_switch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the active context of circle layout — circle_switch","text":"radial coord_radial() object defines global parameters coord_radial across plots layout. parameters start, end, direction, expand inherited applied uniformly plots within layout. parameters theta r.axis.inside always ignored set \"x\" TRUE, respectively, plots. direction single string \"inward\" \"outward\", indicating direction plot added. outward: plot added inner outer. inward: plot added outer inner. get activated circle_layout()? single number string plot elements layout. NULL, remove active context. ... dots future extensions must empty.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_switch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the active context of circle layout — circle_switch","text":"circle_switch object can added circle_layout().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/circle_switch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine the active context of circle layout — circle_switch","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) rownames(small_mat) <- paste0(\"row\", seq_len(nrow(small_mat))) colnames(small_mat) <- paste0(\"column\", seq_len(ncol(small_mat))) circle_discrete(small_mat) + ggalign() + geom_tile(aes(y = .column_index, fill = value)) + scale_fill_viridis_c() + align_dendro(aes(color = branch), k = 3L) + scale_color_brewer(palette = \"Dark2\")"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/continuous_limits.html","id":null,"dir":"Reference","previous_headings":"","what":"Set continuous limits for the layout — continuous_limits","title":"Set continuous limits for the layout — continuous_limits","text":"align continuous axes, important keep limits consistent across plots layout. can set limits passing function directly limits xlim/ylim argument, using ... . Alternatively, can add continuous_limits() object layout. quad_layout() function, must specify x/y arguments. layouts, pass limits using ... directly.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/continuous_limits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set continuous limits for the layout — continuous_limits","text":"","code":"continuous_limits(..., x = waiver(), y = waiver())"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/continuous_limits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set continuous limits for the layout — continuous_limits","text":"... list two numeric values, specifying left/lower limit right/upper limit scale. x, y ..., specifically quad_layout().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_link.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a plot to connect selected observations — cross_link","title":"Add a plot to connect selected observations — cross_link","text":"Add plot connect selected observations","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_link.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a plot to connect selected observations — cross_link","text":"","code":"cross_link( link, data = waiver(), ..., on_top = TRUE, obs_size = 1, inherit_index = NULL, inherit_panel = NULL, inherit_nobs = NULL, size = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_link.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a plot to connect selected observations — cross_link","text":"link link_draw() object defines draw links, link_line(). data dataset use layout. default, fortify_matrix() convert data matrix. argument allows change layout data. specified, original data used. ... Additional arguments passed fortify_matrix(). on_top boolean value indicating whether draw link top plot panel (TRUE) (FALSE). obs_size single numeric value indicates size single observation, ranging (0, 1]. inherit_index boolean value indicating whether inherit ordering index. TRUE, match layout ordering index data names. inherit_panel boolean value indicating whether inherit panel group. TRUE, match layout panel data names. inherit_nobs boolean value indicating whether inherit number observations (nobs). TRUE, data input must compatible layout data. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_link.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 Specification","title":"Add a plot to connect selected observations — cross_link","text":"cross_link function initializes ggplot object initialize data. Using scheme_data() change internal data needed.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_mark.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a plot to annotate observations — cross_mark","title":"Add a plot to annotate observations — cross_mark","text":"Add plot annotate observations","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_mark.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a plot to annotate observations — cross_mark","text":"","code":"cross_mark( mark, data = waiver(), ..., obs_size = 1, inherit_index = NULL, inherit_panel = NULL, inherit_nobs = NULL, size = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_mark.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a plot to annotate observations — cross_mark","text":"mark mark_draw() object define draw links. Like mark_line(), mark_tetragon(). Note names pair links used define panel names must unique. data dataset use layout. default, fortify_matrix() convert data matrix. argument allows change layout data. specified, original data used. ... Additional arguments passed fortify_matrix(). obs_size single numeric value indicates size single observation, ranging (0, 1]. inherit_index boolean value indicating whether inherit ordering index. TRUE, match layout ordering index data names. inherit_panel boolean value indicating whether inherit panel group. TRUE, match layout panel data names. inherit_nobs boolean value indicating whether inherit number observations (nobs). TRUE, data input must compatible layout data. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_mark.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 Specification","title":"Add a plot to annotate observations — cross_mark","text":"cross_mark function initializes ggplot object. underlying data contains following columns: .panel: panel aligned axis. means x-axis vertical stack layout (including top bottom annotation), y-axis horizontal stack layout (including left right annotation). .names (vec_names()) .index (vec_size()/NROW()): character names (applicable names exists) integer index original data. .hand: factor levels c(\"left\", \"right\") horizontal stack layouts, c(\"top\", \"bottom\") vertical stack layouts, indicating position linked observations. can use scheme_data() modify internal data needed.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_none.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset layout ordering and panel group — cross_none","title":"Reset layout ordering and panel group — cross_none","text":"Reset layout ordering panel group","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_none.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset layout ordering and panel group — cross_none","text":"","code":"cross_none( data = waiver(), ..., inherit_index = NULL, inherit_panel = NULL, inherit_nobs = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/cross_none.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reset layout ordering and panel group — cross_none","text":"data dataset use layout. default, fortify_matrix() convert data matrix. argument allows change layout data. specified, original data used. ... Additional arguments passed fortify_matrix(). inherit_index boolean value indicating whether inherit ordering index. TRUE, match layout ordering index data names. inherit_panel boolean value indicating whether inherit panel group. TRUE, match layout panel data names. inherit_nobs boolean value indicating whether inherit number observations (nobs). TRUE, data input must compatible layout data.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-link_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the links to connect a pair of observations — .link_draw","title":"Define the links to connect a pair of observations — .link_draw","text":"base version link_draw(), optimized performance. function serves foundation building link_* functions manage drawing links pairs observations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-link_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the links to connect a pair of observations — .link_draw","text":"","code":".link_draw(.draw, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-link_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the links to connect a pair of observations — .link_draw","text":".draw function used draw links. function must return grob() object. function return valid grob, drawing occur. input data function list, item data frame containing coordinates pair observations. ... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-mark_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the links to connect the marked observations — .mark_draw","title":"Define the links to connect the marked observations — .mark_draw","text":"base version mark_draw, designed performance optimization. function used build mark_* functions manage drawing links marked observations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-mark_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the links to connect the marked observations — .mark_draw","text":"","code":".mark_draw(.draw, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/dot-mark_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the links to connect the marked observations — .mark_draw","text":".draw function used draw links. function must return grob() object. function return valid grob, nothing drawn. input data function contains list, item list two data frames: one panel side coordinates (\"panel\") one marked observations coordinates (\"link\"). ... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Key glyphs for legends — draw_key_draw","title":"Key glyphs for legends — draw_key_draw","text":"geom associated function draws key geom needs displayed legend. functions called draw_key_*(), * stands name respective key glyph. key glyphs can customized individual geoms providing geom key_glyph argument. draw_key_draw function provides interface custom key glyphs used geom_draw().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Key glyphs for legends — draw_key_draw","text":"","code":"draw_key_draw(data, params, size)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Key glyphs for legends — draw_key_draw","text":"data single row data frame containing scaled aesthetics display key params list additional parameters supplied geom. size Width height key mm.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Key glyphs for legends — draw_key_draw","text":"grid grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Key glyphs for legends — draw_key_draw","text":"","code":"p <- ggplot(economics, aes(date, psavert, color = \"savings rate\")) # key glyphs can be specified by their name p + geom_line(key_glyph = \"timeseries\") # key glyphs can be specified via their drawing function p + geom_line(key_glyph = draw_key_rect)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw2.html","id":null,"dir":"Reference","previous_headings":"","what":"Key glyphs for legends — draw_key_draw2","title":"Key glyphs for legends — draw_key_draw2","text":"geom associated function draws key geom needs displayed legend. functions called draw_key_*(), * stands name respective key glyph. key glyphs can customized individual geoms providing geom key_glyph argument. draw_key_draw2 function provides interface custom key glyphs used geom_draw2().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Key glyphs for legends — draw_key_draw2","text":"","code":"draw_key_draw2(data, params, size)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Key glyphs for legends — draw_key_draw2","text":"data single row data frame containing scaled aesthetics display key params list additional parameters supplied geom. size Width height key mm.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Key glyphs for legends — draw_key_draw2","text":"grid grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/draw_key_draw2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Key glyphs for legends — draw_key_draw2","text":"","code":"p <- ggplot(economics, aes(date, psavert, color = \"savings rate\")) # key glyphs can be specified by their name p + geom_line(key_glyph = \"timeseries\") # key glyphs can be specified via their drawing function p + geom_line(key_glyph = draw_key_rect)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_curve.html","id":null,"dir":"Reference","previous_headings":"","what":"Theme curve elements — element_curve","title":"Theme curve elements — element_curve","text":"Draw curve.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_curve.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Theme curve elements — element_curve","text":"","code":"element_curve( colour = NULL, linewidth = NULL, linetype = NULL, lineend = NULL, color = NULL, curvature = NULL, angle = NULL, ncp = NULL, shape = NULL, arrow = NULL, arrow.fill = NULL, inherit.blank = FALSE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_curve.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Theme curve elements — element_curve","text":"colour, color Line/border colour. Color alias colour. linewidth Line/border size mm. linetype Line type. integer (0:8), name (blank, solid, dashed, dotted, dotdash, longdash, twodash), string even number (eight) hexadecimal digits give lengths consecutive positions string. lineend Line end Line end style (round, butt, square) curvature numeric value giving amount curvature. Negative values produce left-hand curves, positive values produce right-hand curves, zero produces straight line. angle numeric value 0 180, giving amount skew control points curve. Values less 90 skew curve towards start point values greater 90 skew curve towards end point. ncp number control points used draw curve. control points creates smoother curve. shape numeric vector values -1 1, control shape curve relative control points. See grid.xspline details. arrow list describing arrow heads place either end curve, produced arrow function. arrow.fill Fill colour arrows. inherit.blank element inherit existence element_blank among parents? TRUE existence blank element among parents cause element blank well. FALSE blank parent element ignored calculating final element state.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_curve.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Theme curve elements — element_curve","text":"element_curve object","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_polygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Theme Polygon elements — element_polygon","title":"Theme Polygon elements — element_polygon","text":"Draw polygon.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_polygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Theme Polygon elements — element_polygon","text":"","code":"element_polygon( fill = NULL, colour = NULL, linewidth = NULL, linetype = NULL, alpha = NULL, lineend = NULL, linejoin = NULL, linemitre = NULL, color = NULL, inherit.blank = FALSE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_polygon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Theme Polygon elements — element_polygon","text":"fill Fill colour. colour, color Line/border colour. Color alias colour. linewidth Line/border size mm. linetype Line type. integer (0:8), name (blank, solid, dashed, dotted, dotdash, longdash, twodash), string even number (eight) hexadecimal digits give lengths consecutive positions string. alpha transparency value 0 (transparent) 1 (opaque), parallel fill. lineend Line end Line end style (round, butt, square) linejoin Line join style (round, mitre, bevel). linemitre Line mitre limit (number greater 1). inherit.blank element inherit existence element_blank among parents? TRUE existence blank element among parents cause element blank well. FALSE blank parent element ignored calculating final element state.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_polygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Theme Polygon elements — element_polygon","text":"element_polygon object","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply a function to the fields of an element object — element_vec","title":"Apply a function to the fields of an element object — element_vec","text":"element object, fields vectorized, others . function allows apply function vectorized fields. following helper functions available: element_rep: Applies rep(). element_rep_len: Applies rep_len(). element_vec_recycle: Applies vec_recycle(). element_vec_rep: Applies vec_rep(). element_vec_rep_each: Applies vec_rep_each(). element_vec_slice: Applies vec_slice().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply a function to the fields of an element object — element_vec","text":"","code":"element_vec(.el, .fn, ...) element_rep(.el, ...) element_rep_len(.el, length.out, ...) element_vec_recycle(.el, size, ...) element_vec_rep(.el, times, ...) element_vec_rep_each(.el, times, ...) element_vec_slice(.el, i, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/element_vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply a function to the fields of an element object — element_vec","text":".el element object. .fn function applied vectorized fields element object. ... Additional arguments passed fn. length.Non-negative integer. desired length output vector. inputs coerced double vector first element taken. Ignored NA invalid. size Desired output size. times vec_rep(), single integer number times repeat entire vector. vec_rep_each(), integer vector number times repeat element x. times recycled size x. integer, character logical vector specifying locations names observations get/set. Specify TRUE index elements (x[]), NULL, FALSE integer() index none (x[NULL]).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.character.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame.character","title":"Build a data frame — fortify_data_frame.character","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame.character","text":"","code":"# S3 method for class 'character' fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL) # S3 method for class 'numeric' fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL) # S3 method for class 'logical' fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL) # S3 method for class 'complex' fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame.character","text":"data object converted data frame. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame.character","text":"data frame following columns: .names: names vector (applicable names exist). value: actual value vector.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.default.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame.default","title":"Build a data frame — fortify_data_frame.default","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.default.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame.default","text":"","code":"# Default S3 method fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.default.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame.default","text":"data object converted data frame. ... Additional arguments passed fortify(). data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.default.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame.default","text":"data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.default.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build a data frame — fortify_data_frame.default","text":"default, calls fortify() build data frame.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame.dendrogram","title":"Build a data frame — fortify_data_frame.dendrogram","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame.dendrogram","text":"","code":"# S3 method for class 'dendrogram' fortify_data_frame( data, ..., priority = \"right\", center = FALSE, type = \"rectangle\", leaf_pos = NULL, leaf_braches = NULL, reorder_branches = TRUE, branch_gap = NULL, root = NULL, double = TRUE, data_arg = caller_arg(data), call = NULL ) # S3 method for class 'hclust' fortify_data_frame(data, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame.dendrogram","text":"data hclust dendrogram object. ... Additional arguments passed dendrogram method. priority string \"left\" \"right\". draw right left, left override right, take \"left\" priority. draw left right, right override left, take \"right\" priority. used align_dendro() provide support facet operation ggplot2. center boolean value. TRUE, nodes plotted centered respect leaves/tips branch. Otherwise (default), plot middle direct child nodes. type string indicates plot type, \"rectangle\" \"triangle\". leaf_pos x-coordinates leaf node. Must length number observations tree. leaf_braches Branches leaf node. Must length number observations tree. Usually come cutree. reorder_branches single boolean value, indicates whether reorder provided leaf_braches based actual index. branch_gap single numeric value indicates gap different branches. root length one string numeric indicates root branch. double single logical value indicating whether horizontal lines doubled segments span multiple branches. TRUE, horizontal lines repeated branch segment spans. FALSE, one horizontal line drawn. used align_dendro() provide support facet operation ggplot2. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame.dendrogram","text":"data frame node coordinates: .panel: Similar panel column, always give correct branch usage ggplot facet. .index: original index tree node label: node label text x y: x-axis y-axis coordinates node branch: branch node . can use column color different groups. panel: panel node , split plot panel using facet_grid, column show panel node . Note: nodes may fall outside panel (two panels), possible NA values column. leaf: logical value indicates whether node leaf.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a data frame — fortify_data_frame.dendrogram","text":"edge: data frame edge coordinates: .panel: Similar panel column, always give correct branch usage ggplot facet. x y: x-axis y-axis coordinates start node edge. xend yend: x-axis y-axis coordinates terminal node edge. branch: branch edge . can use column color different groups. panel1 panel2: panel1 panel2 columns functionality panel, specifically edge data correspond nodes edge.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.dendrogram.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Build a data frame — fortify_data_frame.dendrogram","text":"","code":"fortify_data_frame(hclust(dist(USArrests), \"ave\")) #> .index label x y branch leaf panel .panel #> 1 9 Florida 1.000000 0.000000 root TRUE #> 2 33 North Carolina 2.000000 0.000000 root TRUE #> 3 NA 1.500000 38.527912 root FALSE #> 4 5 California 3.000000 0.000000 root TRUE #> 5 20 Maryland 4.000000 0.000000 root TRUE #> 6 3 Arizona 5.000000 0.000000 root TRUE #> 7 31 New Mexico 6.000000 0.000000 root TRUE #> 8 NA 5.500000 13.896043 root FALSE #> 9 NA 4.750000 15.453120 root FALSE #> 10 NA 3.875000 28.012211 root FALSE #> 11 8 Delaware 7.000000 0.000000 root TRUE #> 12 1 Alabama 8.000000 0.000000 root TRUE #> 13 18 Louisiana 9.000000 0.000000 root TRUE #> 14 NA 8.500000 15.454449 root FALSE #> 15 NA 7.750000 16.891499 root FALSE #> 16 13 Illinois 10.000000 0.000000 root TRUE #> 17 32 New York 11.000000 0.000000 root TRUE #> 18 NA 10.500000 6.236986 root FALSE #> 19 22 Michigan 12.000000 0.000000 root TRUE #> 20 28 Nevada 13.000000 0.000000 root TRUE #> 21 NA 12.500000 13.297368 root FALSE #> 22 NA 11.500000 18.417331 root FALSE #> 23 NA 9.625000 26.363428 root FALSE #> 24 2 Alaska 14.000000 0.000000 root TRUE #> 25 24 Mississippi 15.000000 0.000000 root TRUE #> 26 40 South Carolina 16.000000 0.000000 root TRUE #> 27 NA 15.500000 21.167192 root FALSE #> 28 NA 14.750000 28.095803 root FALSE #> 29 NA 12.187500 39.394633 root FALSE #> 30 NA 8.031250 44.283922 root FALSE #> 31 NA 4.765625 77.605024 root FALSE #> 32 47 Washington 17.000000 0.000000 root TRUE #> 33 37 Oregon 18.000000 0.000000 root TRUE #> 34 50 Wyoming 19.000000 0.000000 root TRUE #> 35 36 Oklahoma 20.000000 0.000000 root TRUE #> 36 46 Virginia 21.000000 0.000000 root TRUE #> 37 NA 20.500000 7.355270 root FALSE #> 38 NA 19.750000 10.736739 root FALSE #> 39 NA 18.875000 12.878100 root FALSE #> 40 NA 17.937500 16.425489 root FALSE #> 41 39 Rhode Island 22.000000 0.000000 root TRUE #> 42 21 Massachusetts 23.000000 0.000000 root TRUE #> 43 30 New Jersey 24.000000 0.000000 root TRUE #> 44 NA 23.500000 11.456439 root FALSE #> 45 NA 22.750000 22.595978 root FALSE #> 46 NA 20.343750 26.713777 root FALSE #> 47 25 Missouri 25.000000 0.000000 root TRUE #> 48 4 Arkansas 26.000000 0.000000 root TRUE #> 49 42 Tennessee 27.000000 0.000000 root TRUE #> 50 NA 26.500000 12.614278 root FALSE #> 51 NA 25.750000 20.198479 root FALSE #> 52 10 Georgia 28.000000 0.000000 root TRUE #> 53 6 Colorado 29.000000 0.000000 root TRUE #> 54 43 Texas 30.000000 0.000000 root TRUE #> 55 NA 29.500000 14.501034 root FALSE #> 56 NA 28.750000 23.972143 root FALSE #> 57 NA 27.250000 29.054195 root FALSE #> 58 NA 23.796875 44.837933 root FALSE #> 59 12 Idaho 31.000000 0.000000 root TRUE #> 60 27 Nebraska 32.000000 0.000000 root TRUE #> 61 17 Kentucky 33.000000 0.000000 root TRUE #> 62 26 Montana 34.000000 0.000000 root TRUE #> 63 NA 33.500000 3.834058 root FALSE #> 64 NA 32.750000 12.438692 root FALSE #> 65 NA 31.875000 15.026107 root FALSE #> 66 35 Ohio 35.000000 0.000000 root TRUE #> 67 44 Utah 36.000000 0.000000 root TRUE #> 68 NA 35.500000 6.637771 root FALSE #> 69 14 Indiana 37.000000 0.000000 root TRUE #> 70 16 Kansas 38.000000 0.000000 root TRUE #> 71 NA 37.500000 3.929377 root FALSE #> 72 7 Connecticut 39.000000 0.000000 root TRUE #> 73 38 Pennsylvania 40.000000 0.000000 root TRUE #> 74 NA 39.500000 8.027453 root FALSE #> 75 NA 38.500000 13.352260 root FALSE #> 76 NA 37.000000 15.122897 root FALSE #> 77 NA 34.437500 20.598507 root FALSE #> 78 11 Hawaii 41.000000 0.000000 root TRUE #> 79 48 West Virginia 42.000000 0.000000 root TRUE #> 80 19 Maine 43.000000 0.000000 root TRUE #> 81 41 South Dakota 44.000000 0.000000 root TRUE #> 82 NA 43.500000 8.537564 root FALSE #> 83 NA 42.750000 10.771175 root FALSE #> 84 34 North Dakota 45.000000 0.000000 root TRUE #> 85 45 Vermont 46.000000 0.000000 root TRUE #> 86 NA 45.500000 13.044922 root FALSE #> 87 23 Minnesota 47.000000 0.000000 root TRUE #> 88 49 Wisconsin 48.000000 0.000000 root TRUE #> 89 15 Iowa 49.000000 0.000000 root TRUE #> 90 29 New Hampshire 50.000000 0.000000 root TRUE #> 91 NA 49.500000 2.291288 root FALSE #> 92 NA 48.750000 10.184218 root FALSE #> 93 NA 47.875000 18.993398 root FALSE #> 94 NA 46.687500 27.779904 root FALSE #> 95 NA 44.718750 33.117815 root FALSE #> 96 NA 42.859375 41.094765 root FALSE #> 97 NA 38.648438 54.746831 root FALSE #> 98 NA 31.222656 89.232093 root FALSE "},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame","title":"Build a data frame — fortify_data_frame","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame","text":"","code":"fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame","text":"data object converted data frame. ... Arguments passed methods. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame","text":"data frame.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame.matrix","title":"Build a data frame — fortify_data_frame.matrix","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame.matrix","text":"","code":"# S3 method for class 'matrix' fortify_data_frame(data, ..., data_arg = caller_arg(data), call = NULL) # S3 method for class 'DelayedMatrix' fortify_data_frame(data, ...) # S3 method for class 'Matrix' fortify_data_frame(data, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame.matrix","text":"data matrix-like object. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame.matrix","text":"Matrix transformed long-form data frame, row represents unique combination matrix indices corresponding values. resulting data frame contain following columns: .row_names .row_index: row names (applicable names exist) integer representing row index original matrix. .column_names .column_index: column names (applicable names exist) column index original matrix. value: actual value.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a data frame — fortify_data_frame.phylo","title":"Build a data frame — fortify_data_frame.phylo","text":"function converts various objects data frame.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a data frame — fortify_data_frame.phylo","text":"","code":"# S3 method for class 'phylo' fortify_data_frame( data, ..., type = \"rectangle\", center = FALSE, tree_type = NULL, tip_pos = NULL, data_arg = caller_arg(data), call = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a data frame — fortify_data_frame.phylo","text":"data hclust dendrogram object. ... dots future extensions must empty. type string indicates plot type, \"rectangle\" \"triangle\". center boolean value. TRUE, nodes plotted centered respect leaves/tips branch. Otherwise (default), plot middle direct child nodes. tree_type single string, one \"phylogram\" \"cladogram\", indicating type tree. phylogram: Represents phylogenetic tree branch lengths indicate evolutionary distance time. cladogram: Represents tree branch lengths used, branches reflect evolutionary time. Usually, need modify . tip_pos x-coordinates tip. Must length number tips tree. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.phylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a data frame — fortify_data_frame.phylo","text":"data frame node coordinates: .index: original index tree tip/node. label: tip/node label text. x y: x-axis y-axis coordinates tip/node. tip: logical value indicates whether current node tip.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_data_frame.phylo.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a data frame — fortify_data_frame.phylo","text":"edge: data frame edge coordinates: x y: x-axis y-axis coordinates start node edge. xend yend: x-axis y-axis coordinates terminal node edge.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.GISTIC.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a matrix from a maftools object — fortify_matrix.GISTIC","title":"Build a matrix from a maftools object — fortify_matrix.GISTIC","text":"Build matrix maftools object","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.GISTIC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a matrix from a maftools object — fortify_matrix.GISTIC","text":"","code":"# S3 method for class 'GISTIC' fortify_matrix( data, ..., n_top = NULL, bands = NULL, ignored_bands = NULL, sample_anno = NULL, remove_empty_samples = TRUE, data_arg = caller_arg(data), call = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.GISTIC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a matrix from a maftools object — fortify_matrix.GISTIC","text":"data GISTIC object. ... dots future extensions must empty. n_top single number indicates many top bands drawn. bands atomic character defines bands draw. ignored_bands atomic character defines bands ignored. sample_anno data frame sample clinical features added. remove_empty_samples single boolean value indicating whether drop samples without genomic alterations. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.GISTIC.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a matrix from a maftools object — fortify_matrix.GISTIC","text":"sample_anno: sample clinical informations provided sample_anno. sample_summary: sample copy number summary informations. See data@cnv.summary details. cytoband_summary: cytoband summary informations. See data@cytoband.summary details. gene_summary: gene summary informations. See data@gene.summary details. summary: data frame summary information. See data@summary details.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.MAF.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a matrix from a maftools object — fortify_matrix.MAF","title":"Build a matrix from a maftools object — fortify_matrix.MAF","text":"Convert MAF object matrix: fortify_matrix.MAF: Extract genomic alterations genes. fortify_matrix.MAF_pathways: Extract genomic alterations pathways. tune.MAF() helps convert MAF object MAF_pathways object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.MAF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a matrix from a maftools object — fortify_matrix.MAF","text":"","code":"# S3 method for class 'MAF' fortify_matrix( data, ..., genes = NULL, n_top = NULL, remove_empty_genes = TRUE, remove_empty_samples = TRUE, collapse_vars = TRUE, use_syn = TRUE, missing_genes = \"error\", data_arg = caller_arg(data), call = NULL ) # S3 method for class 'MAF_pathways' fortify_matrix( data, ..., pathdb = \"smgbp\", remove_empty_pathways = TRUE, remove_empty_samples = TRUE, data_arg = caller_arg(data), call = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.MAF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a matrix from a maftools object — fortify_matrix.MAF","text":"data MAF object. ... dots future extensions must empty. genes atomic character defines genes draw. n_top single number indicates many top genes drawn. remove_empty_genes single boolean value indicats whether drop genes without genomic alterations. remove_empty_samples single boolean value indicats whether drop samples without genomic alterations. collapse_vars single boolean value indicating whether collapse multiple alterations sample gene single value \"Multi_Hit\". Alternatively, can provide single string indicates collapsed values. use_syn single boolean value indicates whether include synonymous variants Classifies SNPs transitions transversions. missing_genes string, either \"error\" \"remove\", specifying action handling missing genes. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user. pathdb string \"smgbp\" \"sigpw\", named list genes define pathways. remove_empty_pathways single boolean value indicats whether drop pathways without genomic alterations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.MAF.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a matrix from a maftools object — fortify_matrix.MAF","text":"fortify_matrix.MAF: gene_summary: gene summary informations. See maftools::getGeneSummary() details. sample_summary: sample summary informations. See maftools::getSampleSummary() details. sample_anno: sample clinical informations. See maftools::getClinicalData() details. n_genes: Total genes. n_samples: Total samples. titv: list data.frames Transitions Transversions summary. See maftools::titv() details. fortify_matrix.MAF_pathways: gene_list: pathway contents. pathway_summary: pathway summary informations. See maftools::pathways() details. sample_summary: sample summary informations. See maftools::getSampleSummary() details. sample_anno: sample clinical informations. See maftools::getClinicalData() details.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.default.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a Matrix — fortify_matrix.default","title":"Build a Matrix — fortify_matrix.default","text":"default, calls .matrix() build matrix.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.default.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a Matrix — fortify_matrix.default","text":"","code":"# Default S3 method fortify_matrix(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.default.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a Matrix — fortify_matrix.default","text":"data object converted matrix. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.default.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a Matrix — fortify_matrix.default","text":"matrix.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a Matrix — fortify_matrix","title":"Build a Matrix — fortify_matrix","text":"function converts various objects matrix format. default, calls .matrix() build matrix.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a Matrix — fortify_matrix","text":"","code":"fortify_matrix(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a Matrix — fortify_matrix","text":"data object converted matrix. ... Additional arguments passed methods. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a Matrix — fortify_matrix","text":"matrix.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.list_upset.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a Matrix for UpSet plot — fortify_matrix.list_upset","title":"Build a Matrix for UpSet plot — fortify_matrix.list_upset","text":"function converts list matrix format suitable creating UpSet plot. always returns matrix horizontal UpSet plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.list_upset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a Matrix for UpSet plot — fortify_matrix.list_upset","text":"","code":"# S3 method for class 'list_upset' fortify_matrix( data, mode = \"distinct\", ..., data_arg = caller_arg(data), call = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.list_upset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a Matrix for UpSet plot — fortify_matrix.list_upset","text":"data list sets. mode string \"distinct\", \"intersect\", \"union\" indicates mode define set intersections. Check https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#upset-mode details. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.list_upset.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a Matrix for UpSet plot — fortify_matrix.list_upset","text":"intersection_sizes: integer vector indicating size intersection. set_sizes: integer vector indicating size set.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a matrix from a matrix — fortify_matrix.matrix","title":"Build a matrix from a matrix — fortify_matrix.matrix","text":"Build matrix matrix","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a matrix from a matrix — fortify_matrix.matrix","text":"","code":"# S3 method for class 'matrix' fortify_matrix(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a matrix from a matrix — fortify_matrix.matrix","text":"data matrix object. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix.html","id":"shape","dir":"Reference","previous_headings":"","what":"shape","title":"Build a matrix from a matrix — fortify_matrix.matrix","text":"upset: fortify_matrix.matrix_upset","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix_upset.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a Matrix for UpSet plot — fortify_matrix.matrix_upset","title":"Build a Matrix for UpSet plot — fortify_matrix.matrix_upset","text":"Converts matrix suitable creating UpSet plot. tune.matrix() helps convert matrix object matrix_upset object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix_upset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a Matrix for UpSet plot — fortify_matrix.matrix_upset","text":"","code":"# S3 method for class 'matrix_upset' fortify_matrix(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix_upset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a Matrix for UpSet plot — fortify_matrix.matrix_upset","text":"data matrix row represents element, column defines set. values matrix indicate whether element part set. non-missing value signifies element exists set. ... Arguments passed fortify_matrix.list_upset mode string \"distinct\", \"intersect\", \"union\" indicates mode define set intersections. Check https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#upset-mode details. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.matrix_upset.html","id":"ggalign-attributes","dir":"Reference","previous_headings":"","what":"ggalign attributes","title":"Build a Matrix for UpSet plot — fortify_matrix.matrix_upset","text":"intersection_sizes: integer vector indicating size intersection. set_sizes: integer vector indicating size set.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a matrix from phylo object — fortify_matrix.phylo","title":"Build a matrix from phylo object — fortify_matrix.phylo","text":"method allows phylo object directly input stack_discrete() circle_discrete(). makes possible add align_phylo() stack independently, align_phylo() requires layout labels.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a matrix from phylo object — fortify_matrix.phylo","text":"","code":"# S3 method for class 'phylo' fortify_matrix(data, ..., data_arg = caller_arg(data), call = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a matrix from phylo object — fortify_matrix.phylo","text":"data phylo object. ... dots future extensions must empty. data_arg argument name data. Developers can use improve messages. used user. call execution environment data arguments method collected, e.g., caller_env(). Developers can use improve messages. used user.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/fortify_matrix.phylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a matrix from phylo object — fortify_matrix.phylo","text":"one-column matrix tip labels values, row names also tip labels.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/free.html","id":null,"dir":"Reference","previous_headings":"","what":"Free from alignment — free_align","title":"Free from alignment — free_align","text":"align_plots try align plot panels, every elements plot, following functions romove restrictions: free_align: want compose plots without alignment panel axes (panel aligned). can wrap plot free_align. free_border: want compose plots without alignment panel borders (still align panels ), can wrap plot free_border. free_lab: want compose plots without alignment axis title, can wrap plot free_lab. free_space: Removing ggplot element sizes aligning. free_vp: Customize viewport aligning. free_guide: want override behaviour overall guides behaviour, can wrap plot free_guide.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/free.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Free from alignment — free_align","text":"","code":"free_align(plot, axes = \"tlbr\") free_border(plot, borders = \"tlbr\") free_guide(plot, guides = \"tlbr\") free_lab(plot, labs = \"tlbr\") free_space(plot, spaces = \"tlbr\") free_vp(plot, x = 0.5, y = 0.5, width = NA, height = NA, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/free.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Free from alignment — free_align","text":"plot ggplot alignpatches object. axes axes aligned? string containing one \"t\", \"l\", \"b\", \"r\". borders border aligned? string containing one \"t\", \"l\", \"b\", \"r\". guides string containing one \"t\", \"l\", \"b\", \"r\" indicates side guide legends collected plot. NULL, guide legends collected. labs axis labs free? string containing one \"t\", \"l\", \"b\", \"r\". spaces border spaces removed? string containing one \"t\", \"l\", \"b\", \"r\". x numeric vector unit object specifying x-location. y numeric vector unit object specifying y-location. width numeric vector unit object specifying width. height numeric vector unit object specifying height. ... Arguments passed grid::viewport default.units string indicating default units use x, y, width, height given numeric vectors. just string numeric vector specifying justification viewport relative (x, y) location. two values, first value specifies horizontal justification second value specifies vertical justification. Possible string values : \"left\", \"right\", \"centre\", \"center\", \"bottom\", \"top\". numeric values, 0 means left alignment 1 means right alignment. gp object class \"gpar\", typically output call function gpar. basically list graphical parameter settings. clip One \"\", \"inherit\", \"\", indicating whether clip extent viewport, inherit clipping region parent viewport, turn clipping altogether. back-compatibility, logical value TRUE corresponds \"\" FALSE corresponds \"inherit\". May also grob (gTree) describes clipping path result call .path. mask One \"none\" (FALSE) \"inherit\" (TRUE) grob (gTree) result call .mask. specifies viewport mask, inherit mask parent, mask, described grob. xscale numeric vector length two indicating minimum maximum x-scale. limits may identical. yscale numeric vector length two indicating minimum maximum y-scale. limits may identical. angle numeric value indicating angle rotation viewport. Positive values indicate amount rotation, degrees, anticlockwise positive x-axis. layout Grid layout object splits viewport subregions. layout.pos.row numeric vector giving rows occupied viewport parent's layout. layout.pos.col numeric vector giving columns occupied viewport parent's layout. name character value uniquely identify viewport pushed onto viewport tree.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/free.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Free from alignment — free_align","text":"free_align: modified version plot free_align class. free_border: modified version plot free_border class. free_guide: modified version plot free_guide class. free_lab: modified version plot free_lab class. free_space: modified version plot free_space class. free_vp: modified version plot free_vp class.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/free.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Free from alignment — free_align","text":"","code":"# directly copied from `patchwork` # Sometimes you have a plot that defies good composition alginment, e.g. due # to long axis labels p1 <- ggplot(mtcars) + geom_bar(aes(y = factor(gear), fill = factor(gear))) + scale_y_discrete( \"\", labels = c( \"3 gears are often enough\", \"But, you know, 4 is a nice number\", \"I would def go with 5 gears in a modern car\" ) ) # When combined with other plots it ends up looking bad p2 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) align_plots(p1, p2, ncol = 1L) # We can fix this be using `free_align` align_plots(free_align(p1), p2, ncol = 1L) # If we still want the panels to be aligned to the right, we can choose to # free only the left side align_plots(free_align(p1, axes = \"l\"), p2, ncol = 1L) # We could use `free_lab` to fix the layout in a different way align_plots(p1, free_lab(p2), ncol = 1L) # `free_border` is similar with `free_lab`, they have a distinction in terms # of placement on either the top or bottom side of the panel. Specifically, # the top side contains the `title` and `subtitle`, while the bottom side # contains the `caption`. free_lab() does not attach these elements in the # panel area. p3 <- ggplot(mtcars) + geom_point(aes(hp, wt, colour = mpg)) + ggtitle(\"Plot 3\") p_axis_top <- ggplot(mtcars) + geom_point(aes(mpg, disp)) + ggtitle(\"Plot axis in top\") + scale_x_continuous(position = \"top\") align_plots(p_axis_top, free_lab(p3)) align_plots(p_axis_top, free_border(p3)) # Another issue is that long labels can occupy much spaces align_plots(NULL, p1, p2, p2) # This can be fixed with `free_space` align_plots(NULL, free_space(p1, \"l\"), p2, p2)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Layer with Grid or Function — geom_draw","title":"Layer with Grid or Function — geom_draw","text":"Draw ggplot2 layer using grob function.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Layer with Grid or Function — geom_draw","text":"","code":"geom_draw( draw, mapping = NULL, data = NULL, type = \"group\", stat = \"identity\", position = \"identity\", ..., na.rm = FALSE, show.legend = FALSE, inherit.aes = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layer with Grid or Function — geom_draw","text":"draw Either grob object function (can purrr-style) accepts least three arguments (data, panel_params coord) returns grob. draw function, used draw_group/draw_panel function Geom ggproto object. always call coord$transform(data, panel_params) inside function draw obtain transformed data plot scales. mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). type single string \"group\" \"panel\", \"group\" draws geoms draw_group, displays multiple observations one geometric object, \"panel\" draws geoms draw_panel, displaying individual graphical objects observation (row). Default: \"group\". stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend. na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Layer with Grid or Function — geom_draw","text":"want combine functionality multiple geoms, can typically achieved preparing data geom inside draw_*() call sending different geoms, collecting output grid::gList (list grobs) draw_group() grid::gTree (grob containing multiple child grobs) draw_panel().","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layer with Grid or Function — geom_draw","text":"","code":"text <- grid::textGrob( \"ggdraw\", x = c(0, 0, 0.5, 1, 1), y = c(0, 1, 0.5, 0, 1), hjust = c(0, 0, 0.5, 1, 1), vjust = c(0, 1, 0.5, 0, 1) ) ggplot(data.frame(x = 1, y = 2)) + geom_draw(text)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":null,"dir":"Reference","previous_headings":"","what":"Layer with customized draw function — geom_draw2","title":"Layer with customized draw function — geom_draw2","text":"Layer customized draw function","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Layer with customized draw function — geom_draw2","text":"","code":"geom_draw2( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., na.rm = FALSE, show.legend = NA, inherit.aes = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layer with customized draw function — geom_draw2","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. ... Additional arguments passed draw aesthetic. na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Layer with customized draw function — geom_draw2","text":"geom_draw2 depends new aesthetics draw, always provided scale_draw_manual(), , can provide list functions define value drawn. ggplot2 aesthetics can used arguments.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Layer with customized draw function — geom_draw2","text":"geom_draw2() understands following aesthetics (required aesthetics bold): draw alpha colour fill group linetype linewidth shape size stroke x y Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\").","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_draw2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layer with customized draw function — geom_draw2","text":"","code":"library(grid) ggplot(data.frame(value = letters[seq_len(5)], y = seq_len(5))) + geom_draw2(aes(x = 1, y = y, draw = value, fill = value)) + scale_draw_manual(values = list( a = function(x, y, width, height, fill) { rectGrob(x, y, width = width, height = height, gp = gpar(fill = fill), default.units = \"native\" ) }, b = function(x, y, width, height, fill) { rectGrob(x, y, width = width, height = height, gp = gpar(fill = fill), default.units = \"native\" ) }, c = function(x, y, width, height, fill) { rectGrob(x, y, width = width, height = height, gp = gpar(fill = fill), default.units = \"native\" ) }, d = function(x, y, width, height, shape) { gList( pointsGrob(x, y, pch = shape), # To ensure the rectangle color is shown in the legends, you # must explicitly provide a color argument and include it in # the `gpar()` of the graphical object rectGrob(x, y, width, height, gp = gpar(col = \"black\", fill = NA) ) ) }, e = function(xmin, xmax, ymin, ymax) { segmentsGrob( xmin, ymin, xmax, ymax, gp = gpar(lwd = 2) ) } )) + scale_fill_brewer(palette = \"Dark2\") + theme_void()"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":null,"dir":"Reference","previous_headings":"","what":"Pie charts — geom_pie","title":"Pie charts — geom_pie","text":"Pie charts","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pie charts — geom_pie","text":"","code":"geom_pie( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., clockwise = TRUE, steps = 100, lineend = \"butt\", linejoin = \"round\", linemitre = 10, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pie charts — geom_pie","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend. clockwise single boolean value indicates clockwise . steps integer indicating number steps generate pie chart radian. Increasing value results smoother pie circular. lineend Line end style (round, butt, square). linejoin Line join style (round, mitre, bevel). linemitre Line mitre limit (number greater 1). na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":"new-aesthetics","dir":"Reference","previous_headings":"","what":"new aesthetics","title":"Pie charts — geom_pie","text":"angle: pie circle angle. angle0: initial pie circle angle. radius: circle radius.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Pie charts — geom_pie","text":"geom_pie() understands following aesthetics (required aesthetics bold): x y angle alpha angle0 colour fill group linetype linewidth radius Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\").","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_pie.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pie charts — geom_pie","text":"","code":"ggplot(data.frame(x = 1:10, y = 1:10, value = 1:10 / sum(1:10))) + geom_pie(aes(x, y, angle = value * 360))"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_rect3d.html","id":null,"dir":"Reference","previous_headings":"","what":"Add z-aesthetic for geom_tile — geom_rect3d","title":"Add z-aesthetic for geom_tile — geom_rect3d","text":"Add z-aesthetic geom_tile","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_rect3d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add z-aesthetic for geom_tile — geom_rect3d","text":"","code":"geom_rect3d( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., lineend = \"butt\", linejoin = \"round\", linemitre = 10, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE ) geom_tile3d( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., lineend = \"butt\", linejoin = \"round\", linemitre = 10, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_rect3d.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add z-aesthetic for geom_tile — geom_rect3d","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend. lineend Line end style (round, butt, square). linejoin Line join style (round, mitre, bevel). linemitre Line mitre limit (number greater 1). na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_rect3d.html","id":"new-aesthetics","dir":"Reference","previous_headings":"","what":"new aesthetics","title":"Add z-aesthetic for geom_tile — geom_rect3d","text":"z: third dimention (z direction). theta: Angle x-axis z-axis.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_rect3d.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Add z-aesthetic for geom_tile — geom_rect3d","text":"geom_rect3d() understands following aesthetics (required aesthetics bold): xmin xmax ymin ymax z alpha colour fill group linetype linewidth Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\"). geom_tile3d() understands following aesthetics (required aesthetics bold): x y z alpha colour fill group height linetype linewidth width Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\").","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_subrect.html","id":null,"dir":"Reference","previous_headings":"","what":"Subdivide Rectangles — geom_subrect","title":"Subdivide Rectangles — geom_subrect","text":"geoms subdivide rectangles shared borders grid. geoms achieve result differ rectangles parameterized: geom_subrect(): Defines rectangles using four corners (xmin, xmax, ymin, ymax). geom_subtile(): Defines rectangles using center (x, y) dimensions (width, height).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_subrect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subdivide Rectangles — geom_subrect","text":"","code":"geom_subrect( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., byrow = TRUE, direction = NULL, lineend = \"butt\", linejoin = \"mitre\", na.rm = FALSE, show.legend = NA, inherit.aes = TRUE ) geom_subtile( mapping = NULL, data = NULL, stat = \"identity\", position = \"identity\", ..., byrow = TRUE, direction = NULL, lineend = \"butt\", linejoin = \"mitre\", na.rm = FALSE, show.legend = NA, inherit.aes = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_subrect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subdivide Rectangles — geom_subrect","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend. byrow single boolean value indicates whether arrange divided rectangles row-major order. direction string specifying arrangement direction: \"h\"(horizontal): Creates single row (one-row layout). \"v\"(vertical): Creates single column (one-column layout). NULL: Automatically determines layout dimensions using logic similar facet_wrap(). lineend Line end style (round, butt, square). linejoin Line join style (round, mitre, bevel). na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_subrect.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Subdivide Rectangles — geom_subrect","text":"geom_subrect() understands following aesthetics (required aesthetics bold): xmin xmax ymin ymax alpha colour fill group linetype linewidth Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\"). geom_subtile() understands following aesthetics (required aesthetics bold): x y alpha colour fill group height linetype linewidth width Learn setting aesthetics vignette(\"ggplot2-specs\", package = \"ggplot2\").","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/geom_subrect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subdivide Rectangles — geom_subrect","text":"","code":"# arranges by row ggplot(data.frame(value = letters[seq_len(5)])) + geom_subtile(aes(x = 1, y = 1, fill = value)) #> `geom_subtile()` subdivide tile into a maximal of 5 rectangles # arranges by column ggplot(data.frame(value = letters[seq_len(9)])) + geom_subtile(aes(x = 1, y = 1, fill = value), byrow = FALSE) #> `geom_subtile()` subdivide tile into a maximal of 9 rectangles # one-row ggplot(data.frame(value = letters[seq_len(4)])) + geom_subtile(aes(x = 1, y = 1, fill = value), direction = \"h\") #> `geom_subtile()` subdivide tile into a maximal of 4 rectangles # one-column ggplot(data.frame(value = letters[seq_len(4)])) + geom_subtile(aes(x = 1, y = 1, fill = value), direction = \"v\") #> `geom_subtile()` subdivide tile into a maximal of 4 rectangles"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign-package.html","id":null,"dir":"Reference","previous_headings":"","what":"ggalign: A 'ggplot2' Extension for Consistent Axis Alignment — ggalign-package","title":"ggalign: A 'ggplot2' Extension for Consistent Axis Alignment — ggalign-package","text":"'ggplot2' extension offers various tools organizing arranging plots. designed consistently align specific axis across multiple 'ggplot' objects, making especially useful plots requiring data order manipulation. typical use case includes organizing combinations like dendrogram heatmap.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"ggalign: A 'ggplot2' Extension for Consistent Axis Alignment — ggalign-package","text":"Maintainer: Yun Peng yunyunp96@163.com (ORCID) Authors: Shixiang Wang w_shixiang@163.com (ORCID)","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":null,"dir":"Reference","previous_headings":"","what":"Add ggplot by Aligning discrete or continuous variable — ggalign","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"ggalign() similar ggplot initializes ggplot data mapping. ggalign() allowing provide data various formats, including matrices, data frames, simple vectors. default, inherit layout. function, apply layout matrix. ggalign() focuses integrating plots layout aligning axes.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"","code":"ggalign( data = waiver(), mapping = aes(), ..., size = NULL, no_axes = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"data following options can used: NULL: data set. waiver(): Inherits data layout matrix. function (including purrr-like lambda syntax): Applied layout matrix transform data use. transform final plot data, please use scheme_data(). matrix, data.frame, atomic vector. mapping Default list aesthetic mappings use plot. specified, must supplied layer added plot. ... Additional arguments passed fortify_data_frame(). size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. no_axes Logical; TRUE, removes axes elements alignment axis using theme_no_axes(). default, use option- \"ggalign.align_no_axes\". active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"ggalign initializes ggplot object. underlying data created using fortify_data_frame(). Please refer details. aligning discrete variables, ggalign() always applies default mapping axis data index layout. Specifically: aes(y = .data$.y) used horizontal stack_layout() (including left right annotations). aes(x = .data$.x) used vertical stack_layout() (including top bottom annotations) circle_layout(). following columns added data frame align discrete variables: .panel: panel aligned axis. Refers x-axis vertical stack_layout() (including top bottom annotations), y-axis horizontal stack_layout() (including left right annotations). .names (vec_names()) .index (vec_size()/NROW()): Character names (available) integer index original data. .x/.y .discrete_x/.discrete_y: Integer indices x/y coordinates, factor data labels (applicable names exist). recommended use .x/.y, .discrete_x/.discrete_y x/y mapping. data inherits quad_layout()/ggheatmap(), additional columns added: .extra_panel: Provides panel information column (left right annotation) row (top bottom annotation). .extra_index: index information column (left right annotation) row (top bottom annotation).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":"discrete-axis-alignment","dir":"Reference","previous_headings":"","what":"Discrete Axis Alignment","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"important note consider rows observations, meaning vec_size(data)/NROW(data) must match number observations along axis used alignment (x-axis vertical stack layout, y-axis horizontal stack layout).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add ggplot by Aligning discrete or continuous variable — ggalign","text":"","code":"ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + ggalign() + geom_point(aes(y = value)) #> → heatmap built with `geom_tile()` ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top(size = 0.5) + align_dendro(k = 3L) + ggalign(data = NULL, size = 0.2) + geom_tile(aes(y = 1L, fill = .panel)) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalignGrob.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a plot grob. — ggalignGrob","title":"Generate a plot grob. — ggalignGrob","text":"Generate plot grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalignGrob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a plot grob. — ggalignGrob","text":"","code":"ggalignGrob(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalignGrob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a plot grob. — ggalignGrob","text":"x object converted grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalignGrob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a plot grob. — ggalignGrob","text":"grob() object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalignGrob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a plot grob. — ggalignGrob","text":"","code":"ggalignGrob(ggplot()) #> TableGrob (20 x 17) \"layout\": 26 grobs #> z cells name grob #> 1 0 ( 1-20, 1-17) background rect[plot.background..rect.3459] #> 2 5 ( 9- 9, 7- 7) spacer zeroGrob[NULL] #> 3 7 (11-11, 7- 7) axis-l zeroGrob[NULL] #> 4 3 (13-13, 7- 7) spacer zeroGrob[NULL] #> 5 6 ( 9- 9, 9- 9) axis-t zeroGrob[NULL] #> 6 1 (11-11, 9- 9) panel gTree[panel-1.gTree.3454] #> 7 9 (13-13, 9- 9) axis-b zeroGrob[NULL] #> 8 4 ( 9- 9,11-11) spacer zeroGrob[NULL] #> 9 8 (11-11,11-11) axis-r zeroGrob[NULL] #> 10 2 (13-13,11-11) spacer zeroGrob[NULL] #> 11 10 ( 8- 8, 9- 9) xlab-t zeroGrob[NULL] #> 12 11 (14-14, 9- 9) xlab-b zeroGrob[NULL] #> 13 12 (11-11, 6- 6) ylab-l zeroGrob[NULL] #> 14 13 (11-11,12-12) ylab-r zeroGrob[NULL] #> 15 14 (11-11,15-15) guide-box-right zeroGrob[NULL] #> 16 15 (11-11, 3- 3) guide-box-left zeroGrob[NULL] #> 17 16 (17-17, 9- 9) guide-box-bottom zeroGrob[NULL] #> 18 17 ( 5- 5, 9- 9) guide-box-top zeroGrob[NULL] #> 19 18 (11-11, 9- 9) guide-box-inside zeroGrob[NULL] #> 20 19 ( 4- 4, 9- 9) subtitle zeroGrob[plot.subtitle..zeroGrob.3456] #> 21 20 ( 3- 3, 9- 9) title zeroGrob[plot.title..zeroGrob.3455] #> 22 21 (18-18, 9- 9) caption zeroGrob[plot.caption..zeroGrob.3457] #> 23 22 ( 7- 7, 9- 9) patch-title-top zeroGrob[NULL] #> 24 23 (11-11, 5- 5) patch-title-left zeroGrob[NULL] #> 25 24 (15-15, 9- 9) patch-title-bottom zeroGrob[NULL] #> 26 25 (11-11,13-13) patch-title-right zeroGrob[NULL]"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Data from the Attribute Attached by ggalign — ggalign_attr","title":"Get Data from the Attribute Attached by ggalign — ggalign_attr","text":"ggalign_attr provides access supplementary information stored attributes layout rendering process. attributes, commonly attached data transformation functions like fortify_matrix() fortify_data_frame(), can include essential details filtered supplementary data inform downstream operations. additional attribute, stores factor levels, can accessed ggalign_lvls.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Data from the Attribute Attached by ggalign — ggalign_attr","text":"","code":"ggalign_attr(x, field = NULL, check = TRUE) ggalign_lvls(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Data from the Attribute Attached by ggalign — ggalign_attr","text":"x Data used, typically inherited layout quad_layout()/ggheatmap() stack_layout() object. field string specifying particular data retrieve attached attribute. NULL, entire attached attribute list returned. check boolean indicating whether check field exists. TRUE, error raised specified field exist.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Data from the Attribute Attached by ggalign — ggalign_attr","text":"ggalign_attr: specified data attached supplementary data NULL unavailable. ggalign_lvls: attached supplementary levels NULL unavailable.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_attr.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Data from the Attribute Attached by ggalign — ggalign_attr","text":"Attributes attached data especially useful input data transformed ways limit access complete dataset. example, fortify_matrix.MAF() might filter mutation data adding attributes retain important context, total number observations, detailed aggregated analyses. Additionally, stores levels Variant_Classification usage.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_data_set.html","id":null,"dir":"Reference","previous_headings":"","what":"Attach supplementary data and levels for ggalign — ggalign_data_set","title":"Attach supplementary data and levels for ggalign — ggalign_data_set","text":"Attach supplementary data levels ggalign","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_data_set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Attach supplementary data and levels for ggalign — ggalign_data_set","text":"","code":"ggalign_data_set(.data, ..., .lvls = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_data_set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Attach supplementary data and levels for ggalign — ggalign_data_set","text":".data Input data layout. ... list data attached. .lvls character vector representing attached levels.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_data_set.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Attach supplementary data and levels for ggalign — ggalign_data_set","text":"Used developers fortify_matrix(), fortify_data_frame(), related methods.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_stat.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the statistics from the layout — ggalign_stat","title":"Get the statistics from the layout — ggalign_stat","text":"Get statistics layout","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_stat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the statistics from the layout — ggalign_stat","text":"","code":"ggalign_stat(x, ...) # S3 method for class 'QuadLayout' ggalign_stat(x, position, ...) # S3 method for class 'StackLayout' ggalign_stat(x, what, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_stat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the statistics from the layout — ggalign_stat","text":"x quad_layout()/ggheatmap() stack_layout() object. ... Arguments passed methods. position string \"top\", \"left\", \"bottom\", \"right\". single number string plot elements stack layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggalign_stat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the statistics from the layout — ggalign_stat","text":"statistics","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggcross.html","id":null,"dir":"Reference","previous_headings":"","what":"Connect two layout crosswise — ggcross","title":"Connect two layout crosswise — ggcross","text":"ggcross resets layout ordering index stack_cross(). allows add align_* objects define new layout ordering index. objects added ggcross use updated layout ordering index. feature particularly useful creating tanglegram visualizations. ggcross() alias ggcross().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggcross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Connect two layout crosswise — ggcross","text":"","code":"ggcross(mapping = aes(), size = NULL, no_axes = NULL, active = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggcross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Connect two layout crosswise — ggcross","text":"mapping Default list aesthetic mappings use plot. specified, must supplied layer added plot. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. no_axes Logical; TRUE, removes axes elements alignment axis using theme_no_axes(). default, use option- \"ggalign.align_no_axes\". active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggcross.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Connect two layout crosswise — ggcross","text":"ggcross() initializes ggplot data mapping. ggcross() always applies default mapping axis data index layout. mapping aes(y = .data$.y) horizontal stack layout (including left right annotation) aes(x = .data$.x) vertical stack layout (including top bottom annotation). data underlying ggplot object contain following columns: .panel: panel aligned axis. Refers x-axis vertical stack_layout() (including top bottom annotations), y-axis horizontal stack_layout() (including left right annotations). .names (vec_names()) .index (vec_size()/NROW()): Character names (available) integer index original data. .hand: factor indicates index groups. .x/.y .discrete_x/.discrete_y: Integer indices x/y coordinates, factor data labels (applicable names exist). recommended use .x/.y, .discrete_x/.discrete_y x/y mapping.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggfree.html","id":null,"dir":"Reference","previous_headings":"","what":"Add ggplot to layout without alignment — ggfree","title":"Add ggplot to layout without alignment — ggfree","text":"ggfree() function allows incorporate ggplot object layout. Unlike ggalign(), aligns every axis value precisely, ggfree() focuses integrating plots layout without enforcing strict axis alignment.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggfree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add ggplot to layout without alignment — ggfree","text":"","code":"ggfree(data = waiver(), ..., size = NULL, active = NULL) # Default S3 method ggfree(data = waiver(), mapping = aes(), ..., size = NULL, active = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggfree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add ggplot to layout without alignment — ggfree","text":"data following options can used: NULL: data set. waiver(): Inherits data layout matrix. function (including purrr-like lambda syntax): Applied layout matrix transform data use. transform final plot data, please use scheme_data(). matrix, data.frame, atomic vector. ... Additional arguments passed fortify_data_frame(). size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. active active() object defines context settings added layout. mapping Default list aesthetic mappings use plot. specified, must supplied layer added plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggfree.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Add ggplot to layout without alignment — ggfree","text":"ggalign initializes ggplot object. underlying data created using fortify_data_frame(). Please refer method details. used quad_layout()/ggheatmap(), data inherited quad_layout() direction aligns discrete variables, following columns added: .extra_panel: Provides panel information column (left right annotation) row (top bottom annotation). .extra_index: index information column (left right annotation) row (top bottom annotation).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggfree.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add ggplot to layout without alignment — ggfree","text":"","code":"ggheatmap(matrix(rnorm(56), nrow = 7)) + anno_top() + align_dendro() + ggfree(mtcars, aes(wt, mpg)) + geom_point() #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggmark.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a plot to annotate selected observations — ggmark","title":"Add a plot to annotate selected observations — ggmark","text":"Add plot annotate selected observations","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggmark.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a plot to annotate selected observations — ggmark","text":"","code":"ggmark( mark, data = waiver(), mapping = aes(), ..., group1 = NULL, group2 = NULL, obs_size = 1, size = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggmark.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a plot to annotate selected observations — ggmark","text":"mark mark_draw() object define draw links. Like mark_line(), mark_tetragon(). Note names pair links used define panel names must unique. data following options can used: NULL: data set. waiver(): Inherits data layout matrix. function (including purrr-like lambda syntax): Applied layout matrix transform data use. transform final plot data, please use scheme_data(). matrix, data.frame, atomic vector. mapping Default list aesthetic mappings use plot. specified, must supplied layer added plot. ... Additional arguments passed fortify_data_frame(). group1, group2 single boolean value indicating whether use panel group information layout paired groups. default, specific observations selected mark, ggmark() automatically connect observations group according layout's defined groups. obs_size single numeric value indicates size single observation, ranging (0, 1]. size relative size plot, can specified unit(). Note circle_layout(), size values interpreted relative sizes, layout type adjusts based available space circular arrangement. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggmark.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Add a plot to annotate selected observations — ggmark","text":"ggmark initializes ggplot object. underlying data created using fortify_data_frame(). Please refer details. addition, following columns added data frame: .panel: panel aligned axis. means x-axis vertical stack layout (including top bottom annotation), y-axis horizontal stack layout (including left right annotation). .names (vec_names()) .index (vec_size()/NROW()): character names (applicable names exists) integer index original data. .hand: factor levels c(\"left\", \"right\") horizontal stack layouts, c(\"top\", \"bottom\") vertical stack layouts, indicating position linked observations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggmark.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a plot to annotate selected observations — ggmark","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) rownames(small_mat) <- paste0(\"row\", seq_len(nrow(small_mat))) colnames(small_mat) <- paste0(\"column\", seq_len(ncol(small_mat))) # mark_line ggheatmap(small_mat) + theme(axis.text.x = element_text(hjust = 0, angle = -60)) + anno_right() + align_kmeans(3L) + ggmark(mark_line(I(1:3) ~ NULL)) + geom_boxplot(aes(.names, value)) + theme(plot.margin = margin(l = 0.1, t = 0.1, unit = \"npc\")) #> → heatmap built with `geom_tile()` # mark_tetragon ggheatmap(small_mat) + theme(axis.text.x = element_text(hjust = 0, angle = -60)) + anno_right() + align_kmeans(3L) + ggmark(mark_tetragon(I(1:3) ~ NULL)) + geom_boxplot(aes(.names, value)) + theme(plot.margin = margin(l = 0.1, t = 0.1, unit = \"npc\")) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an OncoPrint — ggoncoplot","title":"Create an OncoPrint — ggoncoplot","text":"ggoncoplot() function generates oncoPrint visualizations display genetic alterations matrix format. function especially useful visualizing complex genomic data, mutations, copy number variations, genomic alterations cancer research.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an OncoPrint — ggoncoplot","text":"","code":"ggoncoplot( data = NULL, mapping = aes(), ..., map_width = NULL, map_height = NULL, reorder_row = reorder_column, reorder_column = TRUE, width = NA, height = NA, filling = waiver(), theme = NULL, active = NULL ) # Default S3 method ggoncoplot( data = NULL, mapping = aes(), ..., map_width = NULL, map_height = NULL, reorder_row = reorder_column, reorder_column = TRUE, width = NA, height = NA, filling = waiver(), theme = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an OncoPrint — ggoncoplot","text":"data character matrix encodes alterations, can use \";\", \":\", \",\", \"|\" separate multiple alterations. mapping Default list aesthetic mappings use main plot layout. specified, must supplied layer added main plot. ... Additional arguments passed fortify_matrix(). map_width, map_height named numeric value defines width/height alterations. reorder_row boolean value indicating whether reorder rows based frequency alterations. can set FALSE, add align_order(~rowSums(!.na(.x)), reverse = TRUE) achieve result. may also need set strit = FALSE align_order() already groups. reorder_column boolean value indicating whether reorder columns based characteristics alterations. can set FALSE, add align_reorder(memo_order) achieve result. may also need set strit = FALSE align_reorder() already groups. width, height relative width/height main plot, can unit object. filling ggheatmap(), \"tile\" can used. theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an OncoPrint — ggoncoplot","text":"HeatmapLayout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create an OncoPrint — ggoncoplot","text":"ggoncoplot() wrapper around ggheatmap() function, designed simplify creation OncoPrint-style visualizations. function automatically processes input character matrix splitting encoded alterations (delimited \";\", \":\", \",\", \"|\") individual genomic events unnesting columns visualization.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggoncoplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an OncoPrint — ggoncoplot","text":"","code":"# A simple example from `ComplexHeatmap` mat <- read.table(textConnection( \"s1,s2,s3 g1,snv;indel,snv,indel g2,,snv;indel,snv g3,snv,,indel;snv\" ), row.names = 1, header = TRUE, sep = \",\", stringsAsFactors = FALSE) ggoncoplot(mat, map_width = c(snv = 0.5), map_height = c(indel = 0.9)) + # Note that guide legends from `geom_tile` and `geom_bar` are different. # Although they appear similar, the internal mechanisms won't collapse # the guide legends. Therefore, we remove the guide legends from # `geom_tile`. guides(fill = \"none\") + anno_top(size = 0.5) + ggalign() + geom_bar(aes(fill = value), data = function(x) { subset(x, !is.na(value)) }) + anno_right(size = 0.5) + ggalign() + geom_bar(aes(fill = value), orientation = \"y\", data = function(x) { subset(x, !is.na(value)) }) & scale_fill_brewer(palette = \"Dark2\", na.translate = FALSE)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggupset.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an UpSet plot — ggupset","title":"Create an UpSet plot — ggupset","text":"ggupset specialized version quad_discrete(), simplifies creation Upset plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggupset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an UpSet plot — ggupset","text":"","code":"ggupset( data = NULL, mapping = aes(), ..., direction = \"h\", point = NULL, line = NULL, rect = NULL, width = NA, height = NA, theme = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggupset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an UpSet plot — ggupset","text":"data Data used create UpSet plot. fortify_matrix() used convert data matrix. Currently, fortify_matrix.list_upset fortify_matrix.matrix_upset suitable creating UpSet plot. mapping Default list aesthetic mappings use main plot layout. specified, must supplied layer added main plot. ... Additional arguments passed fortify_matrix(). direction string indicating direction UpSet plot, \"h\"(horizontal) \"v\"(vertical). vertical UpSet plot, columns matrix correspond sets, rows correspond intersections. default, horizontal UpSet plot used, rows matrix correspond sets columns correspond intersections. point list parameters passed geom_point(). line list parameters passed geom_line(). rect list parameters passed geom_rect(). width, height relative width/height main plot, can unit object. theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggupset.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Create an UpSet plot — ggupset","text":"data input converted matrix using fortify_matrix(), data underlying main plot contain following columns: .panel_x .panel_y: column row panel groups. .x .y: integer index x y coordinates .discrete_x .discrete_y: factor data labels (applicable .row_names .column_names exists). .row_names .column_names: character row column names original matrix (applicable names exist). .row_index .column_index: row column index original matrix. value: actual matrix value.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggupset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an UpSet plot — ggupset","text":"","code":"set.seed(123) lt <- list( a = sample(letters, 5), b = sample(letters, 10), c = sample(letters, 15) ) ggupset(tune(lt)) + scale_fill_manual(values = c(\"#F0F0F0\", \"white\"), guide = \"none\") + scale_color_manual(values = c(\"grey\", \"black\"), guide = \"none\") + anno_top() + ggalign(data = function(d) ggalign_attr(d, \"intersection_sizes\")) + ggplot2::geom_bar(aes(y = .data$value), stat = \"identity\") + anno_right() + ggalign(data = function(d) ggalign_attr(d, \"set_sizes\")) + ggplot2::geom_bar(aes(x = .data$value), stat = \"identity\", orientation = \"y\" )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggwrap.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrap Arbitrary Graphics to ggplot — ggwrap","title":"Wrap Arbitrary Graphics to ggplot — ggwrap","text":"ggwrap() function allows non-ggplot2 elements converted compliant representation use align_plots(). useful adding graphics can converted grob patch() method.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggwrap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrap Arbitrary Graphics to ggplot — ggwrap","text":"","code":"ggwrap(plot, ..., align = \"panel\", on_top = FALSE, clip = TRUE, vp = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggwrap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrap Arbitrary Graphics to ggplot — ggwrap","text":"plot graphic can converted grob using patch(). ... Additional arguments passed patch() method. align string specifying area place plot: \"full\" full area, \"plot\" full plotting area (including axis label), \"panel\" actual area data drawn. on_top single boolean value indicates whether graphic plot put frontmost. Note: graphic plot always put background. clip single boolean value indicating whether grob clipped expand outside designated area. vp viewport object, can use define plot area.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggwrap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrap Arbitrary Graphics to ggplot — ggwrap","text":"wrapped_plot object can directly placed align_plots().","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/ggwrap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrap Arbitrary Graphics to ggplot — ggwrap","text":"","code":"library(grid) ggwrap(rectGrob(gp = gpar(fill = \"goldenrod\")), align = \"full\") + inset(rectGrob(gp = gpar(fill = \"steelblue\")), align = \"panel\") + inset(textGrob(\"Here are some text\", gp = gpar(color = \"black\")), align = \"panel\" ) p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) + ggtitle(\"Plot 1\") align_plots(p1, ggwrap( ~ plot(mtcars$mpg, mtcars$disp), mar = c(0, 2, 0, 0), bg = NA ))"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/hclust2.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate Tree Structures with Hierarchical Clustering — hclust2","title":"Generate Tree Structures with Hierarchical Clustering — hclust2","text":"Generate Tree Structures Hierarchical Clustering","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/hclust2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate Tree Structures with Hierarchical Clustering — hclust2","text":"","code":"hclust2( matrix, distance = \"euclidean\", method = \"complete\", use_missing = \"pairwise.complete.obs\" )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/hclust2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate Tree Structures with Hierarchical Clustering — hclust2","text":"matrix numeric matrix, data frame. distance string distance measure used. must one \"euclidean\", \"maximum\", \"manhattan\", \"canberra\", \"binary\" \"minkowski\". Correlation coefficient can also used, including \"pearson\", \"spearman\" \"kendall\". way, 1 - cor used distance. addition, can also provide dist object directly function return dist object. Use NULL, want calculate distance. method string agglomeration method used. (unambiguous abbreviation ) one \"ward.D\", \"ward.D2\", \"single\", \"complete\", \"average\" (= UPGMA), \"mcquitty\" (= WPGMA), \"median\" (= WPGMC) \"centroid\" (= UPGMC). can also provide function accepts calculated distance (input matrix distance NULL) returns hclust object. Alternative, can supply object can coerced hclust. use_missing optional character string giving method computing covariances presence missing values. must (abbreviation ) one strings \"everything\", \".obs\", \"complete.obs\", \"na..complete\", \"pairwise.complete.obs\". used distance correlation coefficient string.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/hclust2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate Tree Structures with Hierarchical Clustering — hclust2","text":"hclust object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/hclust2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate Tree Structures with Hierarchical Clustering — hclust2","text":"","code":"hclust2(dist(USArrests), method = \"ward.D\") #> #> Call: #> stats::hclust(d = d, method = method) #> #> Cluster method : ward.D #> Distance : euclidean #> Number of objects: 50 #>"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a heatmap — heatmap_layout","title":"Create a heatmap — heatmap_layout","text":"heatmap_layout specialized version quad_discrete(), simplifies creation heatmap plots integrating essential elements standard heatmap layout, ensuring appropriate data mapping visualization layers automatically applied. ggheatmap alias heatmap_layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a heatmap — heatmap_layout","text":"","code":"heatmap_layout( data = NULL, mapping = aes(), ..., width = NA, height = NA, filling = waiver(), theme = NULL, active = NULL )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a heatmap — heatmap_layout","text":"data Default dataset use layout. specified, must supplied plot added layout. default, try inherit parent layout. fortify_matrix() used convert data matrix. mapping Default list aesthetic mappings use main plot layout. specified, must supplied layer added main plot. ... Additional arguments passed fortify_matrix(). width, height relative width/height main plot, can unit object. filling single string \"raster\" \"tile\" indicate filling style. default, waiver() used, means input matrix 20,000 cells (nrow * ncol > 20000), geom_raster() used performance efficiency; smaller matrices, geom_tile() used. customize filling style, set NULL. backward compatibility, single boolean value acceptable: TRUE means waiver(), FALSE means NULL. default, classic heatmap color scheme scale_fill_gradient2(low = \"blue\", high = \"red\") utilized continuous values. can use options \"ggalign.heatmap_continuous_fill\" \"ggalign.heatmap_discrete_fill\" modify default heatmap body filling color scale. See scale_fill_continuous() scale_fill_discrete() details option settings. theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. active active() object defines context settings added layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a heatmap — heatmap_layout","text":"HeatmapLayout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Create a heatmap — heatmap_layout","text":"data input converted matrix using fortify_matrix(), data underlying main plot contain following columns: .panel_x .panel_y: column row panel groups. .x .y: integer index x y coordinates .discrete_x .discrete_y: factor data labels (applicable .row_names .column_names exists). .row_names .column_names: character row column names original matrix (applicable names exist). .row_index .column_index: row column index original matrix. value: actual matrix value.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/heatmap_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a heatmap — heatmap_layout","text":"","code":"ggheatmap(1:10) #> → heatmap built with `geom_tile()` ggheatmap(letters) #> → heatmap built with `geom_tile()` ggheatmap(matrix(rnorm(81), nrow = 9L)) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/inset.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a ggplot inset — inset","title":"Create a ggplot inset — inset","text":"Create ggplot inset","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/inset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a ggplot inset — inset","text":"","code":"inset(plot, ..., align = \"panel\", on_top = TRUE, clip = TRUE, vp = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/inset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a ggplot inset — inset","text":"plot graphic can converted grob using patch(). ... Additional arguments passed patch() method. align string specifying area place plot: \"full\" full area, \"plot\" full plotting area (including axis label), \"panel\" actual area data drawn. on_top single boolean value indicates whether graphic plot put frontmost. Note: graphic plot always put background. clip single boolean value indicating whether grob clipped expand outside designated area. vp viewport object, can use define plot area.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/inset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a ggplot inset — inset","text":"patch_inset object, can added ggplot.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/inset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a ggplot inset — inset","text":"","code":"library(grid) p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p1 + inset(p2, vp = viewport(0.6, 0.6, just = c(0, 0), width = 0.4, height = 0.4 ))"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/is_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Reports whether x is layout object — is_layout","title":"Reports whether x is layout object — is_layout","text":"Reports whether x layout object","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/is_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reports whether x is layout object — is_layout","text":"","code":"is_layout(x) is_quad_layout(x) is_stack_layout(x) is_stack_cross(x) is_circle_layout(x) is_heatmap_layout(x) is_ggheatmap(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/is_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reports whether x is layout object — is_layout","text":"x object test.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/is_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reports whether x is layout object — is_layout","text":"single boolean value.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/is_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reports whether x is layout object — is_layout","text":"","code":"is_layout(ggheatmap(1:10)) #> [1] TRUE # for quad_layout() is_quad_layout(quad_alignb(1:10)) #> [1] TRUE is_quad_layout(quad_alignh(1:10)) #> [1] TRUE is_quad_layout(quad_alignv(1:10)) #> [1] TRUE is_quad_layout(quad_free(mtcars)) #> [1] TRUE # for stack_layout() is_stack_layout(stack_discrete(\"h\", 1:10)) #> [1] TRUE is_stack_layout(stack_continuous(\"h\", 1:10)) #> [1] TRUE # for heatmap_layout() is_heatmap_layout(ggheatmap(1:10)) #> [1] TRUE is_ggheatmap(ggheatmap(1:10)) #> [1] TRUE"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layer_order.html","id":null,"dir":"Reference","previous_headings":"","what":"Change the layer adding order — layer_order","title":"Change the layer adding order — layer_order","text":"function allows change order layers added ggplot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layer_order.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change the layer adding order — layer_order","text":"","code":"layer_order(layer, order = 0)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layer_order.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change the layer adding order — layer_order","text":"layer layer geometry object added. order integer indicating position layer added. <= 0, layer added beginning. greater number plot layers, added end.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layer_order.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change the layer adding order — layer_order","text":"layer_order object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layer_order.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Change the layer adding order — layer_order","text":"","code":"ggplot(faithfuld, aes(waiting, eruptions)) + geom_raster(aes(fill = density)) + geom_point(color = \"red\", size = 1) ggplot(faithfuld, aes(waiting, eruptions)) + geom_raster(aes(fill = density)) + layer_order(geom_point(color = \"red\", size = 1))"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout-operator.html","id":null,"dir":"Reference","previous_headings":"","what":"Layout operator — layout-operator","title":"Layout operator — layout-operator","text":"+: Adds elements active plot active layout. &: Applies elements plots layout. -: Adds elements multiple plots layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout-operator.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layout operator — layout-operator","text":"e1 quad_layout()/ggheatmap() stack_layout() object. e2 object added plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout-operator.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Layout operator — layout-operator","text":"modified Layout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout-operator.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Layout operator — layout-operator","text":"+ operator straightforward used needed. order reduce code repetition ggalign provides two operators adding ggplot elements (geoms, themes, facets, etc.) multiple/plots quad_layout()/ggheatmap() stack_layout() object: - &.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout-operator.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layout operator — layout-operator","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) ggheatmap(small_mat) + anno_top() + ggalign() + geom_point(aes(y = value)) #> → heatmap built with `geom_tile()` # `&` operator apply it to all plots ggheatmap(small_mat) + anno_top() + align_dendro() & theme(panel.border = element_rect( colour = \"red\", fill = NA, linewidth = unit(2, \"mm\") )) #> → heatmap built with `geom_tile()` # If the active layout is the annotation stack, the `-` operator will only # add the elements to all plots in the active annotation stack: ggheatmap(small_mat) + anno_left(size = 0.2) + align_dendro(aes(color = branch), k = 3L) + align_dendro(aes(color = branch), k = 3L) - # Modify the the color scales of all plots in the left annotation scale_color_brewer(palette = \"Dark2\") #> → heatmap built with `geom_tile()` # If the active layout is the `stack_layout()` itself, `-` # applies the elements to all plots in the layout except the nested # `ggheatmap()`/`quad_layout()`. stack_alignv(small_mat) + align_dendro() + ggtitle(\"I'm from the parent stack\") + ggheatmap() + # remove any active context stack_active() + align_dendro() + ggtitle(\"I'm from the parent stack\") - # Modify the the color scales of all plots in the stack layout except the # heatmap layout scale_color_brewer(palette = \"Dark2\") - # set the background of all plots in the stack layout except the heatmap # layout theme(plot.background = element_rect(fill = \"red\")) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify components of the layout — layout_annotation","title":"Modify components of the layout — layout_annotation","text":"modify theme layout","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify components of the layout — layout_annotation","text":"","code":"layout_annotation(theme = waiver(), ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify components of the layout — layout_annotation","text":"theme theme() object used customize various elements plot, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. ... dots future extensions must empty.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_annotation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Modify components of the layout — layout_annotation","text":"guides, panel.border, background always used even nested alignpatches object. title, subtitle, caption, margins added top-level alignpatches object .","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify components of the layout — layout_annotation","text":"","code":"p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p3 <- ggplot(mtcars) + geom_bar(aes(gear)) + facet_wrap(~cyl) align_plots( p1 + theme(plot.background = element_blank()), p2 + theme(plot.background = element_blank()), p3 + theme(plot.background = element_blank()) ) + layout_annotation( theme = theme(plot.background = element_rect(fill = \"red\")) )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_design.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the grid to compose plots in — layout_design","title":"Define the grid to compose plots in — layout_design","text":"control different plots laid , need add layout design specification. nesting grids, layout scoped current nesting level.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_design.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the grid to compose plots in — layout_design","text":"","code":"layout_design( ncol = waiver(), nrow = waiver(), byrow = waiver(), widths = waiver(), heights = waiver(), design = waiver(), guides = NA )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_design.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the grid to compose plots in — layout_design","text":"ncol, nrow dimensions grid create - NULL use logic facet_wrap() set dimensions byrow FALSE plots filled column-major order. widths, heights relative widths heights column row grid. get repeated match dimensions grid. special value NA behave 1null unit unless fixed aspect plot inserted case allow dimension expand contract match aspect ratio content. design Specification location areas layout. Can either specified text string concatenating calls area() together. guides string one \"t\", \"l\", \"b\", \"r\" indicating side guide legends collected. Defaults waiver(), inherits parent layout. parent layout, NULL provided, guides collected.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_design.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define the grid to compose plots in — layout_design","text":"layout_design object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_design.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define the grid to compose plots in — layout_design","text":"","code":"p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p3 <- ggplot(mtcars) + geom_bar(aes(gear)) + facet_wrap(~cyl) align_plots(p1, p2, p3) + layout_design(nrow = 1L) align_plots(p1, p2, p3) + layout_design(ncol = 1L)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_expand.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Expansion for the Layout — layout_expand","title":"Set Expansion for the Layout — layout_expand","text":"align axes, important keep expansion consistent across plots layout. can add layout_expand object layout. quad_layout() function, must specify x y arguments. layouts, can pass expansion values using ... directly.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_expand.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Expansion for the Layout — layout_expand","text":"","code":"layout_expand(..., x = waiver(), y = waiver())"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_expand.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Expansion for the Layout — layout_expand","text":"... list range expansion constants, used add padding around data ensure placed distance away axes. Use convenience function expansion() generate values. x, y ..., specifically quad_layout().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_title.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate the whole layout — layout_title","title":"Annotate the whole layout — layout_title","text":"Annotate whole layout","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_title.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate the whole layout — layout_title","text":"","code":"layout_title(title = waiver(), subtitle = waiver(), caption = waiver())"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_title.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate the whole layout — layout_title","text":"title text title. subtitle text subtitle plot displayed title. caption text caption displayed bottom-right plot default.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_title.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Annotate the whole layout — layout_title","text":"layout_title object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/layout_title.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Annotate the whole layout — layout_title","text":"","code":"p1 <- ggplot(mtcars) + geom_point(aes(mpg, disp)) p2 <- ggplot(mtcars) + geom_boxplot(aes(gear, disp, group = gear)) p3 <- ggplot(mtcars) + geom_bar(aes(gear)) + facet_wrap(~cyl) align_plots(p1, p2, p3) + layout_title(title = \"I'm title\")"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the links to connect a pair of observations — link_draw","title":"Define the links to connect a pair of observations — link_draw","text":"function allows users define links pair observations, facilitating visualization connections related data points.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the links to connect a pair of observations — link_draw","text":"","code":"link_draw(.draw, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the links to connect a pair of observations — link_draw","text":".draw function used draw links. function must return grob() object. function return valid grob, drawing occur. input data function include data frame coordinates pair observations linked. ... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_line.html","id":null,"dir":"Reference","previous_headings":"","what":"Link the paired observations with a line — link_line","title":"Link the paired observations with a line — link_line","text":"Link paired observations line","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_line.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Link the paired observations with a line — link_line","text":"","code":"link_line(..., .element = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_line.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Link the paired observations with a line — link_line","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. .element element_line() object. Vectorized fields recycled match total number groups, can wrap element () recycle match drawing groups. drawing groups typically correspond product number observations sides, pair observations linked single line.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_tetragon.html","id":null,"dir":"Reference","previous_headings":"","what":"Link the paired observations with a quadrilateral — link_tetragon","title":"Link the paired observations with a quadrilateral — link_tetragon","text":"Link paired observations quadrilateral","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_tetragon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Link the paired observations with a quadrilateral — link_tetragon","text":"","code":"link_tetragon(..., .element = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/link_tetragon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Link the paired observations with a quadrilateral — link_tetragon","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. .element element_polygon() object. Vectorized fields recycled match total number groups, can wrap element () recycle match drawing groups. drawing groups usually defined groups, differ defined group observations separated linked single quadrilateral. cases, number drawing groups larger number defined groups.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_draw.html","id":null,"dir":"Reference","previous_headings":"","what":"Define the links to connect the marked observations — mark_draw","title":"Define the links to connect the marked observations — mark_draw","text":"function allows users define links marked observations plot panel (e.g., creating visual connections related data), help explain observations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_draw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define the links to connect the marked observations — mark_draw","text":"","code":"mark_draw(.draw, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_draw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define the links to connect the marked observations — mark_draw","text":".draw function used draw links. function must return grob() object. function return valid grob, nothing drawn. input data function must contain two arguments: data frame panel side coordinates data frame marked observation coordinates. ... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_line.html","id":null,"dir":"Reference","previous_headings":"","what":"Link the observations and the panel with a line — mark_line","title":"Link the observations and the panel with a line — mark_line","text":"Link observations panel line","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_line.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Link the observations and the panel with a line — mark_line","text":"","code":"mark_line(..., .element = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_line.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Link the observations and the panel with a line — mark_line","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. .element element_line() object. Vectorized fields recycled match total number groups, can wrap element () recycle match drawing groups. drawing groups typically correspond number observations, observation linked plot panel.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_tetragon.html","id":null,"dir":"Reference","previous_headings":"","what":"Link the observations and the panel with a quadrilateral — mark_tetragon","title":"Link the observations and the panel with a quadrilateral — mark_tetragon","text":"Link observations panel quadrilateral","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_tetragon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Link the observations and the panel with a quadrilateral — mark_tetragon","text":"","code":"mark_tetragon(..., .element = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_tetragon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Link the observations and the panel with a quadrilateral — mark_tetragon","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. .element element_polygon() object. Vectorized fields recycled match total number groups, can wrap element () recycle match drawing groups. drawing groups usually defined groups, differ defined group observations separated linked single quadrilateral. cases, number drawing groups larger number defined groups.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_triangle.html","id":null,"dir":"Reference","previous_headings":"","what":"Link the observations and the panel with a triangle — mark_triangle","title":"Link the observations and the panel with a triangle — mark_triangle","text":"Link observations panel triangle","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_triangle.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Link the observations and the panel with a triangle — mark_triangle","text":"","code":"mark_triangle(..., orientation = \"plot\", .element = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/mark_triangle.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Link the observations and the panel with a triangle — mark_triangle","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. orientation single string, either \"plot\" \"observation\", indicating base triangle. .element element_polygon() object. Vectorized fields recycled match total number groups, can wrap element () recycle match drawing groups. orientation \"plot\", drawing groups typically correspond number observations. orientation \"observation\", drawing groups usually match defined groups, differ defined group observations separated linked single triangle. case, number drawing groups larger number defined groups.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/memo_order.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort matrix for better visualization — memo_order","title":"Sort matrix for better visualization — memo_order","text":"Helper function used order Oncoplot samples. Typically, use combination align_reorder(), e.g., align_reorder(memo_order).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/memo_order.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort matrix for better visualization — memo_order","text":"","code":"memo_order(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/memo_order.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort matrix for better visualization — memo_order","text":"x matrix, NA values treated empty.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/memo_order.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sort matrix for better visualization — memo_order","text":"vector ordering weights.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/new_tune.html","id":null,"dir":"Reference","previous_headings":"","what":"Change the shape of the input object — new_tune","title":"Change the shape of the input object — new_tune","text":"new_tune: Creates new object wrapping scalar list specified attributes class. tune_data: Retrieves original input data.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/new_tune.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change the shape of the input object — new_tune","text":"","code":"new_tune(x, ..., class = character()) tune_data(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/new_tune.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change the shape of the input object — new_tune","text":"x R object. ... Additional attributes passed structure(). class character vector specifying class name added.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/no_expansion.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove scale expansion — no_expansion","title":"Remove scale expansion — no_expansion","text":"Remove scale expansion","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/no_expansion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove scale expansion — no_expansion","text":"","code":"no_expansion(borders = \"tlbr\")"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/no_expansion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove scale expansion — no_expansion","text":"borders border removed? string containing one \"t\", \"l\", \"b\", \"r\", \"x\", \"y\".","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/no_expansion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove scale expansion — no_expansion","text":"object can added ggplot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/order2.html","id":null,"dir":"Reference","previous_headings":"","what":"Ordering Permutation — order2","title":"Ordering Permutation — order2","text":"order2 returns permutation rearranges first argument ascending order.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/order2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ordering Permutation — order2","text":"","code":"order2(x) # S3 method for class 'hclust' order2(x) # S3 method for class 'dendrogram' order2(x) # S3 method for class 'ser_permutation_vector' order2(x) # S3 method for class 'ser_permutation' order2(x) # S3 method for class 'phylo' order2(x) # S3 method for class 'memo_weights' order2(x)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/order2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ordering Permutation — order2","text":"x objects can extracting ordering.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/order2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ordering Permutation — order2","text":"integer vector unless inputs 2^31 elements, double vector.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/order2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Ordering Permutation — order2","text":"","code":"order2(hclust2(matrix(rnorm(100L), nrow = 10L))) #> [1] 5 6 2 3 9 1 4 8 7 10"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/pair_links.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create pairs of observation groups — pair_links","title":"Helper function to create pairs of observation groups — pair_links","text":"ggmark() cross_link() allow users add links observations. functions help define linked observations. selected pairs either linked together, group pair linked separately plot area. pair_links: Helper function create pairs observation groups. range_link: Helper function create range observations.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/pair_links.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create pairs of observation groups — pair_links","text":"","code":"pair_links(..., .handle_missing = \"error\", .reorder = NULL) range_link(point1, point2)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/pair_links.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create pairs of observation groups — pair_links","text":"... list formulas, side formula integer character index original data, range_link() object defining linked observations. Use NULL indicate link side. can also combine wrapping single list(). left-hand side formula exists, can input directly. integer indices, wrap () use ordering layout. can also use waiver() inherit values group. .handle_missing string \"error\" \"remove\" indicates action handling missing observations. .reorder string \"hand1\" \"hand2\" indicating whether reorder input links follow specified layout ordering. point1, point2 single integer character index, defining lower higher bounds range. integer indices, wrap () indicate ordered index layout.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/pair_links.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create pairs of observation groups — pair_links","text":"","code":"x <- pair_links( # group on the left hand only c(\"a\", \"b\"), # normally, integer index will be interpreted as the index of the # origianl data 1:2, # wrapped with `I()` indicate` the integer index is ordering of the # layout I(1:2), range_link(1, 6), range_link(\"a\", \"b\"), # group on the right hand only ~ 1:2, ~ c(\"a\", \"b\"), ~ range_link(1, 6), # group on the both side range_link(1, 6) ~ c(\"a\", \"b\"), # waiver() indicates the right hand is the same of the left hand range_link(1, 6) ~ waiver(), # the same for the left hand waiver() ~ 1:2, ~NULL # an empty link ) x #> #> A total of 12 pairs of link groups #> #> hand1 ~ hand2 #> 1: c(\"a\", \"b\") ~ #> 2: 1:2 ~ #> 3: I(1:2) ~ #> 4: range_link(1, 6) ~ #> 5: range_link(\"a\", \"b\") ~ #> 6: ~ 1:2 #> 7: ~ c(\"a\", \"b\") #> 8: ~ range_link(1, 6) #> 9: range_link(1, 6) ~ c(\"a\", \"b\") #> 10: range_link(1, 6) ~ waiver() #> 11: waiver() ~ 1:2 #> 12: ~ #> #> A total of 14 link groups # we can modify it as usual list x[[1]] <- NULL # remove the first link x$a <- ~LETTERS x #> #> A total of 12 pairs of link groups #> #> hand1 ~ hand2 #> 1: 1:2 ~ #> 2: I(1:2) ~ #> 3: range_link(1, 6) ~ #> 4: range_link(\"a\", \"b\") ~ #> 5: ~ 1:2 #> 6: ~ c(\"a\", \"b\") #> 7: ~ range_link(1, 6) #> 8: range_link(1, 6) ~ c(\"a\", \"b\") #> 9: range_link(1, 6) ~ waiver() #> 10: waiver() ~ 1:2 #> 11: ~ #> a: ~ c(A, B, ..., Z) #> #> A total of 14 link groups # modify with a list x[1:2] <- list(~ c(\"a\", \"b\"), ~ range_link(\"a\", \"b\")) x #> #> A total of 12 pairs of link groups #> #> hand1 ~ hand2 #> 1: ~ c(\"a\", \"b\") #> 2: ~ range_link(\"a\", \"b\") #> 3: range_link(1, 6) ~ #> 4: range_link(\"a\", \"b\") ~ #> 5: ~ 1:2 #> 6: ~ c(\"a\", \"b\") #> 7: ~ range_link(1, 6) #> 8: range_link(1, 6) ~ c(\"a\", \"b\") #> 9: range_link(1, 6) ~ waiver() #> 10: waiver() ~ 1:2 #> 11: ~ #> a: ~ c(A, B, ..., Z) #> #> A total of 14 link groups"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.Heatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.Heatmap","title":"Convert Object into a Grob — patch.Heatmap","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.Heatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.Heatmap","text":"","code":"# S3 method for class 'Heatmap' patch(x, ..., device = NULL) # S3 method for class 'HeatmapList' patch(x, ..., device = NULL) # S3 method for class 'HeatmapAnnotation' patch(x, ..., device = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.Heatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.Heatmap","text":"x object converted grob. ... Additional arguments passed draw(). device function opens graphics device temporary rendering. default -screen, -memory device based pdf device, default device may satisfactory using custom fonts.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.Heatmap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.Heatmap","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.alignpatches.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.alignpatches","title":"Convert Object into a Grob — patch.alignpatches","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.alignpatches.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.alignpatches","text":"","code":"# S3 method for class 'alignpatches' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.alignpatches.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.alignpatches","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.alignpatches.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.alignpatches","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.formula.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.formula","title":"Convert Object into a Grob — patch.formula","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.formula.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.formula","text":"","code":"# S3 method for class 'formula' patch(x, ..., device = NULL, name = NULL) # S3 method for class '`function`' patch(x, ..., device = NULL, name = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.formula.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.formula","text":"x object converted grob. ... Graphical Parameters passed par(). device function opens graphics device grid.echo() work . default -screen, -memory device based pdf device. default device may satisfactory using custom fonts. name character identifier.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.formula.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.formula","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.ggplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.ggplot","title":"Convert Object into a Grob — patch.ggplot","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.ggplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.ggplot","text":"","code":"# S3 method for class 'ggplot' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.ggplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.ggplot","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.ggplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.ggplot","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.grob","title":"Convert Object into a Grob — patch.grob","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.grob","text":"","code":"# S3 method for class 'grob' patch(x, ...) # S3 method for class 'gList' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.grob","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.grob","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch","title":"Convert Object into a Grob — patch","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch","text":"","code":"patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch","text":"x object converted grob. ... Additional arguments passed specific methods.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.patch","title":"Convert Object into a Grob — patch.patch","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.patch","text":"","code":"# S3 method for class 'patch' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.patch","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.patch","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch_ggplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.patch_ggplot","title":"Convert Object into a Grob — patch.patch_ggplot","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch_ggplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.patch_ggplot","text":"","code":"# S3 method for class 'patch_ggplot' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch_ggplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.patch_ggplot","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patch_ggplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.patch_ggplot","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patchwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.patchwork","title":"Convert Object into a Grob — patch.patchwork","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patchwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.patchwork","text":"","code":"# S3 method for class 'patchwork' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patchwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.patchwork","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.patchwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.patchwork","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.pheatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.pheatmap","title":"Convert Object into a Grob — patch.pheatmap","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.pheatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.pheatmap","text":"","code":"# S3 method for class 'pheatmap' patch(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.pheatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.pheatmap","text":"x object converted grob. ... used currently.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.pheatmap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.pheatmap","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.recordedplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.recordedplot","title":"Convert Object into a Grob — patch.recordedplot","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.recordedplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.recordedplot","text":"","code":"# S3 method for class 'recordedplot' patch(x, ..., device = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.recordedplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.recordedplot","text":"x object converted grob. ... used currently. device function opens graphics device grid.echo() work . default -screen, -memory device based pdf device. default device may satisfactory using custom fonts.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.recordedplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.recordedplot","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.trellis.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Object into a Grob — patch.trellis","title":"Convert Object into a Grob — patch.trellis","text":"patch() function used ggwrap() inset() convert objects grob.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.trellis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Object into a Grob — patch.trellis","text":"","code":"# S3 method for class 'trellis' patch(x, ..., device = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.trellis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Object into a Grob — patch.trellis","text":"x object converted grob. ... Arguments passed grid::grid.grabExpr warn integer specifying amount warnings emit. 0 means warnings, 1 means warn certain grab faithfully represent original scene. 2 means warn possibility grab faithfully represent original scene. wrap logical indicating output captured. TRUE, non-grob element display list captured wrapping grob. wrap.grobs logical indicating whether, wrapping elements (wrap=TRUE), wrap grobs (just wrap viewports). width,height Size device used temporary rendering. device function opens graphics device temporary rendering. default -screen, -memory device based pdf device, default device may satisfactory using custom fonts.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch.trellis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Object into a Grob — patch.trellis","text":"grob object.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":null,"dir":"Reference","previous_headings":"","what":"Add patch titles to plot borders — patch_titles","title":"Add patch titles to plot borders — patch_titles","text":"function extends ggplot2's title functionality, allowing add titles border plot: top, left, bottom, right.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add patch titles to plot borders — patch_titles","text":"","code":"patch_titles( top = waiver(), left = waiver(), bottom = waiver(), right = waiver() )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add patch titles to plot borders — patch_titles","text":"top, left, bottom, right string specifying title added top, left, bottom, right border plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add patch titles to plot borders — patch_titles","text":"labels object added ggplot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add patch titles to plot borders — patch_titles","text":"appearance alignment patch titles can customized using theme(): plot.patch_title/plot.patch_title.*: Controls text appearance patch titles. default, plot.patch_title inherit plot.title, settings border inherit plot.patch_title, exception angle property, inherited. plot.patch_title.position/plot.patch_title.position.*: Determines alignment patch titles. default, plot.patch_title.position inherit plot.title.position, settings border inherit plot.patch_title. value \"panel\" aligns patch titles plot panels. Setting \"plot\" aligns patch title entire plot (excluding margins plot tags).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/patch_titles.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add patch titles to plot borders — patch_titles","text":"","code":"ggplot(mtcars) + geom_point(aes(mpg, disp)) + patch_titles( top = \"I'm top patch title\", left = \"I'm left patch title\", bottom = \"I'm bottom patch title\", right = \"I'm right patch title\" )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/plus-ggalign_plot-ANY-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Add custom objects to ggalign plot — +,ggalign_plot,ANY-method","title":"Add custom objects to ggalign plot — +,ggalign_plot,ANY-method","text":"Add custom objects ggalign plot","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/plus-ggalign_plot-ANY-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add custom objects to ggalign plot — +,ggalign_plot,ANY-method","text":"","code":"# S4 method for class 'ggalign_plot,ANY' e1 + e2"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_active.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine the Active Context of Quad-Layout — quad_active","title":"Determine the Active Context of Quad-Layout — quad_active","text":"quad_active: Sets active context quad_layout()/ggheatmap() . quad_anno: Sets active context specified annotation stack based position argument. anno_top: special case quad_anno position = \"top\". anno_left: special case quad_anno position = \"left\". anno_bottom: special case quad_anno position = \"bottom\". anno_right: special case quad_anno position = \"right\".","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_active.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the Active Context of Quad-Layout — quad_active","text":"","code":"quad_active(width = NULL, height = NULL) quad_anno( position, size = NULL, free_guides = waiver(), initialize = NULL, what = waiver() ) anno_top( size = NULL, free_guides = waiver(), initialize = NULL, what = waiver() ) anno_left( size = NULL, free_guides = waiver(), initialize = NULL, what = waiver() ) anno_bottom( size = NULL, free_guides = waiver(), initialize = NULL, what = waiver() ) anno_right( size = NULL, free_guides = waiver(), initialize = NULL, what = waiver() )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_active.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the Active Context of Quad-Layout — quad_active","text":"width, height relative width/height main plot, can unit object. position string \"top\", \"left\", \"bottom\", \"right\" indicates annotation stack activated. size numeric value unit object set total height/width annotation stack. position \"top\" \"bottom\", size sets total height annotation. position \"left\" \"right\", size sets total width annotation. free_guides Override guides collection behavior specified quad_layout()/ggheatmap() annotation stack. initialize boolean indicating whether annotation stack initialized already. default, annotation stack layout attempt initialize data compatible. set TRUE, data quad_layout()/ggheatmap() incompatible annotation stack, data used stack. get activated annotation stack? single number string plot elements layout. NULL, remove active context.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_active.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the Active Context of Quad-Layout — quad_active","text":"object can added quad_layout()/ggheatmap().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_active.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine the Active Context of Quad-Layout — quad_active","text":"default, quad_anno() attempts initialize annotation stack layout using data quad_layout()/ggheatmap(). However, situations want use different data annotation stack, can set initialize = FALSE provide custom stack_layout().","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_init.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize Quad-Layout Annotation — quad_init","title":"Initialize Quad-Layout Annotation — quad_init","text":"function deprecated, can add stack_layout() directly.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_init.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize Quad-Layout Annotation — quad_init","text":"","code":"quad_init(position, data = waiver(), ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange plots in the quad-side of a main plot — quad_layout","title":"Arrange plots in the quad-side of a main plot — quad_layout","text":"function arranges plots around quad-sides main plot, aligning horizontal vertical axes, can handle either discrete continuous variables. xlim provided, continuous variable required aligned vertical direction. Otherwise, discrete variable required aligned. ylim provided, continuous variable required aligned horizontal direction. Otherwise, discrete variable required aligned. quad_discrete special case xlim ylim provided. quad_continuous special case xlim ylim provided. historical reasons, following aliases available: quad_alignh: Align discrete variables horizontal direction continuous variables vertical direction. quad_alignv: Align discrete variables vertical direction continuous variables horizontal direction. quad_alignb alias quad_discrete. quad_free alias quad_continuous.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange plots in the quad-side of a main plot — quad_layout","text":"","code":"quad_layout( data = waiver(), mapping = aes(), xlim = waiver(), ylim = waiver(), ..., theme = NULL, active = NULL, width = NA, height = NA ) quad_alignh(..., ylim = waiver()) quad_alignv(..., xlim = waiver()) quad_discrete( data = waiver(), mapping = aes(), ..., theme = NULL, active = NULL, width = NA, height = NA ) quad_continuous( data = waiver(), mapping = aes(), xlim = NULL, ylim = NULL, ..., theme = NULL, active = NULL, width = NA, height = NA )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange plots in the quad-side of a main plot — quad_layout","text":"data Default dataset use layout. specified, must supplied plot added layout. default, attempt inherit parent layout. xlim ylim provided, data frame required, fortify_data_frame() used convert data data frame. inherited annotation stack, transposition applied. Otherwise, matrix required, fortify_matrix() used convert data matrix. inherited column annotation stack, data transposed. mapping Default list aesthetic mappings use main plot layout. specified, must supplied layer added main plot. xlim, ylim continuous_limits() object specifying left/lower limit right/upper limit scale. Used align continuous axis. ... Additional arguments passed fortify_data_frame() fortify_matrix(). theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. active active() object defines context settings added layout. width, height relative width/height main plot, can unit object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange plots in the quad-side of a main plot — quad_layout","text":"QuadLayout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_layout.html","id":"ggplot-specification","dir":"Reference","previous_headings":"","what":"ggplot2 specification","title":"Arrange plots in the quad-side of a main plot — quad_layout","text":"either xlim ylim provided, data input converted matrix using fortify_matrix(), data underlying main plot contain following columns: .panel_x .panel_y: column row panel groups. .x .y: integer index x y coordinates .discrete_x .discrete_y: factor data labels (applicable .row_names .column_names exists). .row_names .column_names: character row column names original matrix (applicable names exist). .row_index .column_index: row column index original matrix. value: actual matrix value. Otherwise, data input used main plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_switch.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine the Active Context of Quad-Layout — quad_switch","title":"Determine the Active Context of Quad-Layout — quad_switch","text":"quad_switch() integrates quad_active() quad_anno() one function ease use. function allows quickly change active context quad_layout() annotations. hmanno alias quad_switch, additional arguments backward compatibility","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_switch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the Active Context of Quad-Layout — quad_switch","text":"","code":"quad_switch( position = NULL, size = NULL, width = NULL, height = NULL, free_guides = waiver(), initialize = NULL, what = waiver() ) hmanno( position = NULL, size = NULL, width = NULL, height = NULL, free_guides = waiver(), initialize = NULL, what = waiver() )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_switch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the Active Context of Quad-Layout — quad_switch","text":"position string \"top\", \"left\", \"bottom\", \"right\" indicates annotation stack activated. NULL, sets active context quad_layout()/ggheatmap() . size numeric value unit object set total height/width annotation stack. position \"top\" \"bottom\", size sets total height annotation. position \"left\" \"right\", size sets total width annotation. width, height relative width/height main plot, can unit object. free_guides Override guides collection behavior specified quad_layout()/ggheatmap() annotation stack. initialize boolean indicating whether annotation stack initialized already. default, annotation stack layout attempt initialize data compatible. set TRUE, data quad_layout()/ggheatmap() incompatible annotation stack, data used stack. get activated annotation stack? single number string plot elements layout. NULL, remove active context.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_switch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the Active Context of Quad-Layout — quad_switch","text":"object can added quad_layout()/ggheatmap().","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/quad_switch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine the Active Context of Quad-Layout — quad_switch","text":"","code":"ggheatmap(matrix(rnorm(81), nrow = 9)) + anno_top() + align_dendro() #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick.html","id":null,"dir":"Reference","previous_headings":"","what":"Rasterize the input object — raster_magick","title":"Rasterize the input object — raster_magick","text":"function rasterizes input graphical objects (e.g., grob, layer, ggplot) optionally processes resulting raster using magick, powerful image manipulation library. allows advanced graphical transformations directly within plotting pipeline.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rasterize the input object — raster_magick","text":"","code":"raster_magick(x, magick = NULL, ..., res = NULL, interpolate = FALSE)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rasterize the input object — raster_magick","text":"x object rasterize, can grob(), layer(), ggplot(), list objects. magick function (purrr-style formula accepted) takes image_read() object input returns object compatible .raster(). can use image_*() functions magick package process raster image. ... used currently. res integer sets desired resolution pixels. interpolate logical value indicating whether linearly interpolate image (alternative use nearest-neighbour interpolation, gives blocky result).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rasterize the input object — raster_magick","text":"object class input.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Rasterize the input object — raster_magick","text":"","code":"# data generated code was copied from `ComplexHeatmap` set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) rownames(small_mat) <- paste0(\"row\", seq_len(nrow(small_mat))) colnames(small_mat) <- paste0(\"column\", seq_len(ncol(small_mat))) ggheatmap(small_mat, aes(.x, .y), filling = NULL) + raster_magick(geom_tile(aes(fill = value)), res = 20) ggheatmap(small_mat, aes(.x, .y), filling = NULL) + # Use `magick::filter_types()` to check available `filter` arguments raster_magick(geom_tile(aes(fill = value)), magick = function(image) { magick::image_resize(image, geometry = \"50%x\", filter = \"Lanczos\" ) } )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick_interal.html","id":null,"dir":"Reference","previous_headings":"","what":"Rasterize the input object — raster_magick_interal","title":"Rasterize the input object — raster_magick_interal","text":"internal function designed implement functionality raster_magick(). assumes input arguments valid perform additional checks.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick_interal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rasterize the input object — raster_magick_interal","text":"","code":".raster_magick(x, ...) # S3 method for class 'Layer' .raster_magick(x, ...) # S3 method for class 'list' .raster_magick(x, ...) # S3 method for class 'ggplot' .raster_magick(x, ...) # S3 method for class 'grob' .raster_magick(x, magick = NULL, ..., res = NULL, interpolate = FALSE) # S3 method for class 'gList' .raster_magick(x, magick = NULL, ..., res = NULL, interpolate = FALSE) # S3 method for class 'ggalignRasterMagick' .raster_magick(x, magick = NULL, ..., res = NULL, interpolate = FALSE) # S3 method for class 'zeroGrob' .raster_magick(x, ...) # Default S3 method .raster_magick(x, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick_interal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rasterize the input object — raster_magick_interal","text":"x object rasterize, can grob(), layer(), ggplot(), list objects. ... used currently. magick function (purrr-style formula accepted) takes image_read() object input returns object compatible .raster(). can use image_*() functions magick package process raster image. res integer sets desired resolution pixels. interpolate logical value indicating whether linearly interpolate image (alternative use nearest-neighbour interpolation, gives blocky result).","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/raster_magick_interal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rasterize the input object — raster_magick_interal","text":"object class input.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/read_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Example Data — read_example","title":"Read Example Data — read_example","text":"function reads example data file. file specified, returns list available example files.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/read_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Example Data — read_example","text":"","code":"read_example(file = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/read_example.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Example Data — read_example","text":"file string representing name example file read. NULL, function return list available example file names.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/read_example.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Example Data — read_example","text":"file NULL, returns character vector available example file names. Otherwise, returns contents specified example file, read R object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/read_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Example Data — read_example","text":"","code":"read_example() #> [1] \"gene_expression.rds\" \"measles.rds\""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. grid gpar, unit","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scale_draw_manual.html","id":null,"dir":"Reference","previous_headings":"","what":"Scale for draw aesthetic — scale_draw_manual","title":"Scale for draw aesthetic — scale_draw_manual","text":"Draw ggplot2 layer using grob function.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scale_draw_manual.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Scale for draw aesthetic — scale_draw_manual","text":"","code":"scale_draw_manual( ..., values, aesthetics = \"draw\", breaks = waiver(), na.value = NA )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scale_draw_manual.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scale for draw aesthetic — scale_draw_manual","text":"... Arguments passed ggplot2::discrete_scale name name scale. Used axis legend title. waiver(), default, name scale taken first mapping used aesthetic. NULL, legend title omitted. labels One : NULL labels waiver() default labels computed transformation object character vector giving labels (must length breaks) expression vector (must length breaks). See ?plotmath details. function takes breaks input returns labels output. Also accepts rlang lambda function notation. limits One : NULL use default scale values character vector defines possible values scale order function accepts existing (automatic) values returns new ones. Also accepts rlang lambda function notation. na.translate Unlike continuous scales, discrete scales can easily show missing values, default. want remove missing values discrete scale, specify na.translate = FALSE. drop unused factor levels omitted scale? default, TRUE, uses levels appear data; FALSE includes levels factor. Please note display every level legend, layer use show.legend = TRUE. guide function used create guide name. See guides() information. call call used construct scale reporting messages. super super class use constructed scale values list functions (including purrr-like lambda syntax) define cell's grob (graphical object) drawn. aesthetics Character string vector character strings listing name(s) aesthetic(s) scale works . can useful, example, apply colour settings colour fill aesthetics time, via aesthetics = c(\"colour\", \"fill\"). breaks One : NULL breaks waiver() default breaks (scale limits) character vector breaks function takes limits input returns breaks output na.value aesthetic value use missing (NA) values","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scale_draw_manual.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Scale for draw aesthetic — scale_draw_manual","text":"want combine functionality multiple geoms, can typically achieved preparing data geom inside draw_*() call sending different geoms, collecting output grid::gList (list grobs) draw_group() grid::gTree (grob containing multiple child grobs) draw_panel().","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scale_draw_manual.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Scale for draw aesthetic — scale_draw_manual","text":"","code":"text <- grid::textGrob( \"ggdraw\", x = c(0, 0, 0.5, 1, 1), y = c(0, 1, 0.5, 0, 1), hjust = c(0, 0, 0.5, 1, 1), vjust = c(0, 1, 0.5, 0, 1) ) ggplot(data.frame(x = 1, y = 2)) + geom_draw(text)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_align.html","id":null,"dir":"Reference","previous_headings":"","what":"Align Specifications in the Layout — scheme_align","title":"Align Specifications in the Layout — scheme_align","text":"scheme_align() function defines align Specifications plots.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_align.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Align Specifications in the Layout — scheme_align","text":"","code":"scheme_align(guides = NA, free_spaces = NA, free_labs = NA)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_align.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Align Specifications in the Layout — scheme_align","text":"guides string one \"t\", \"l\", \"b\", \"r\" indicating side guide legends collected. Defaults waiver(), inherits parent layout. parent layout, guides collected. NULL, guides collected. free_spaces string one \"t\", \"l\", \"b\", \"r\" indicating border spaces removed. Defaults waiver(), inherits parent layout. parent, default NULL, meaning spaces removed. Usually want apply whole layout, instead individual plots. free_labs string one \"t\", \"l\", \"b\", \"r\" indicating axis titles free alignment. Defaults waiver(), inherits parent layout. parent layout, axis titles aligned. NULL, axis titles aligned.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_align.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Align Specifications in the Layout — scheme_align","text":"scheme_align object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_align.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Align Specifications in the Layout — scheme_align","text":"","code":"set.seed(123) mat <- matrix(rnorm(72), nrow = 8) # used in the layout, define the default action for all plots in the layout ggheatmap(mat) - scheme_align(guides = NULL) + anno_right() + align_dendro(aes(color = branch), k = 3) #> → heatmap built with `geom_tile()` # You can also add it for a single plot ggheatmap(mat) - # for all plots in the layout, we default won't collect any guide legends scheme_align(guides = NULL) + # for the heatmap body, we collect guide legends in the right # note, the guide legends will be collected to the right side of the # layout which will overlap the legends in the right annotation scheme_align(guides = \"r\") + anno_right() + align_dendro(aes(color = branch), k = 3) #> → heatmap built with `geom_tile()` # to avoid overlapping, we can also collect the guide legends in the # right annotation ggheatmap(mat) - scheme_align(guides = NULL) + scheme_align(guides = \"r\") + anno_right() + align_dendro(aes(color = branch), k = 3) + scheme_align(guides = \"r\") #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot data Specifications — scheme_data","title":"Plot data Specifications — scheme_data","text":"Transforms plot data. Many functions package require specific data format align observations, scheme_data() helps reformat data frames needed.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot data Specifications — scheme_data","text":"","code":"scheme_data(data, inherit = FALSE)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot data Specifications — scheme_data","text":"data function transform plot data rendering. Acceptable values include: NULL: action taken. waiver(): Inherits parent layout. function purrr-style formula: Used transform plot data, accept data frame return data frame. can apply parent layout scheme_data function, using inherit argument. Use hook modify data geoms layout created (matrix data, melted long format data frame) rendering ggplot2. returned data must data frame ggplot. inherit single boolean value indicates whether apply parent scheme_data first apply specified scheme_data plot. Defaults FALSE.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot data Specifications — scheme_data","text":"Defaults attempt inherit parent layout actual data inherited parent layout, one exception: align_dendro(), inherit scheme_data default.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_theme.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot default theme — scheme_theme","title":"Plot default theme — scheme_theme","text":"scheme_theme() serves default theme always overridden theme() settings applied directly plot. default theme (scheme_theme()) applied first, followed specific theme() settings, even theme() added scheme_theme().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_theme.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot default theme — scheme_theme","text":"","code":"scheme_theme( ..., line, rect, text, title, aspect.ratio, axis.title, axis.title.x, axis.title.x.top, axis.title.x.bottom, axis.title.y, axis.title.y.left, axis.title.y.right, axis.text, axis.text.x, axis.text.x.top, axis.text.x.bottom, axis.text.y, axis.text.y.left, axis.text.y.right, axis.text.theta, axis.text.r, axis.ticks, axis.ticks.x, axis.ticks.x.top, axis.ticks.x.bottom, axis.ticks.y, axis.ticks.y.left, axis.ticks.y.right, axis.ticks.theta, axis.ticks.r, axis.minor.ticks.x.top, axis.minor.ticks.x.bottom, axis.minor.ticks.y.left, axis.minor.ticks.y.right, axis.minor.ticks.theta, axis.minor.ticks.r, axis.ticks.length, axis.ticks.length.x, axis.ticks.length.x.top, axis.ticks.length.x.bottom, axis.ticks.length.y, axis.ticks.length.y.left, axis.ticks.length.y.right, axis.ticks.length.theta, axis.ticks.length.r, axis.minor.ticks.length, axis.minor.ticks.length.x, axis.minor.ticks.length.x.top, axis.minor.ticks.length.x.bottom, axis.minor.ticks.length.y, axis.minor.ticks.length.y.left, axis.minor.ticks.length.y.right, axis.minor.ticks.length.theta, axis.minor.ticks.length.r, axis.line, axis.line.x, axis.line.x.top, axis.line.x.bottom, axis.line.y, axis.line.y.left, axis.line.y.right, axis.line.theta, axis.line.r, legend.background, legend.margin, legend.spacing, legend.spacing.x, legend.spacing.y, legend.key, legend.key.size, legend.key.height, legend.key.width, legend.key.spacing, legend.key.spacing.x, legend.key.spacing.y, legend.frame, legend.ticks, legend.ticks.length, legend.axis.line, legend.text, legend.text.position, legend.title, legend.title.position, legend.position, legend.position.inside, legend.direction, legend.byrow, legend.justification, legend.justification.top, legend.justification.bottom, legend.justification.left, legend.justification.right, legend.justification.inside, legend.location, legend.box, legend.box.just, legend.box.margin, legend.box.background, legend.box.spacing, panel.background, panel.border, panel.spacing, panel.spacing.x, panel.spacing.y, panel.grid, panel.grid.major, panel.grid.minor, panel.grid.major.x, panel.grid.major.y, panel.grid.minor.x, panel.grid.minor.y, panel.ontop, plot.background, plot.title, plot.title.position, plot.subtitle, plot.caption, plot.caption.position, plot.tag, plot.tag.position, plot.tag.location, plot.margin, strip.background, strip.background.x, strip.background.y, strip.clip, strip.placement, strip.text, strip.text.x, strip.text.x.bottom, strip.text.x.top, strip.text.y, strip.text.y.left, strip.text.y.right, strip.switch.pad.grid, strip.switch.pad.wrap, complete = FALSE, validate = TRUE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_theme.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot default theme — scheme_theme","text":"... theme() object additional element specifications part base ggplot2. general, also defined element tree argument. Splicing list also supported. line line elements (element_line()) rect rectangular elements (element_rect()) text text elements (element_text()) title title elements: plot, axes, legends (element_text(); inherits text) aspect.ratio aspect ratio panel axis.title, axis.title.x, axis.title.y, axis.title.x.top, axis.title.x.bottom, axis.title.y.left, axis.title.y.right labels axes (element_text()). Specify axes' labels (axis.title), labels plane (using axis.title.x axis.title.y), individually axis (using axis.title.x.bottom, axis.title.x.top, axis.title.y.left, axis.title.y.right). axis.title.*.* inherits axis.title.* inherits axis.title, turn inherits text axis.text, axis.text.x, axis.text.y, axis.text.x.top, axis.text.x.bottom, axis.text.y.left, axis.text.y.right, axis.text.theta, axis.text.r tick labels along axes (element_text()). Specify axis tick labels (axis.text), tick labels plane (using axis.text.x axis.text.y), individually axis (using axis.text.x.bottom, axis.text.x.top, axis.text.y.left, axis.text.y.right). axis.text.*.* inherits axis.text.* inherits axis.text, turn inherits text axis.ticks, axis.ticks.x, axis.ticks.x.top, axis.ticks.x.bottom, axis.ticks.y, axis.ticks.y.left, axis.ticks.y.right, axis.ticks.theta, axis.ticks.r tick marks along axes (element_line()). Specify tick marks (axis.ticks), ticks plane (using axis.ticks.x axis.ticks.y), individually axis (using axis.ticks.x.bottom, axis.ticks.x.top, axis.ticks.y.left, axis.ticks.y.right). axis.ticks.*.* inherits axis.ticks.* inherits axis.ticks, turn inherits line axis.minor.ticks.x.top, axis.minor.ticks.x.bottom, axis.minor.ticks.y.left, axis.minor.ticks.y.right, axis.minor.ticks.theta, axis.minor.ticks.r minor tick marks along axes (element_line()). axis.minor.ticks.*.* inherit corresponding major ticks axis.ticks.*.*. axis.ticks.length, axis.ticks.length.x, axis.ticks.length.x.top, axis.ticks.length.x.bottom, axis.ticks.length.y, axis.ticks.length.y.left, axis.ticks.length.y.right, axis.ticks.length.theta, axis.ticks.length.r length tick marks (unit) axis.minor.ticks.length, axis.minor.ticks.length.x, axis.minor.ticks.length.x.top, axis.minor.ticks.length.x.bottom, axis.minor.ticks.length.y, axis.minor.ticks.length.y.left, axis.minor.ticks.length.y.right, axis.minor.ticks.length.theta, axis.minor.ticks.length.r length minor tick marks (unit), relative axis.ticks.length provided rel(). axis.line, axis.line.x, axis.line.x.top, axis.line.x.bottom, axis.line.y, axis.line.y.left, axis.line.y.right, axis.line.theta, axis.line.r lines along axes (element_line()). Specify lines along axes (axis.line), lines plane (using axis.line.x axis.line.y), individually axis (using axis.line.x.bottom, axis.line.x.top, axis.line.y.left, axis.line.y.right). axis.line.*.* inherits axis.line.* inherits axis.line, turn inherits line legend.background background legend (element_rect(); inherits rect) legend.margin margin around legend (margin()) legend.spacing, legend.spacing.x, legend.spacing.y spacing legends (unit). legend.spacing.x & legend.spacing.y inherit legend.spacing can specified separately legend.key background underneath legend keys (element_rect(); inherits rect) legend.key.size, legend.key.height, legend.key.width size legend keys (unit); key background height & width inherit legend.key.size can specified separately legend.key.spacing, legend.key.spacing.x, legend.key.spacing.y spacing legend keys given unit. Spacing horizontal (x) vertical (y) direction inherit legend.key.spacing can specified separately. legend.frame frame drawn around bar (element_rect()). legend.ticks tick marks shown along bars axes (element_line()) legend.ticks.length length tick marks legend (unit) legend.axis.line lines along axes legends (element_line()) legend.text legend item labels (element_text(); inherits text) legend.text.position placement legend text relative legend keys bars (\"top\", \"right\", \"bottom\" \"left\"). legend text placement might incompatible legend's direction guides. legend.title title legend (element_text(); inherits title) legend.title.position placement legend title relative main legend (\"top\", \"right\", \"bottom\" \"left\"). legend.position default position legends (\"none\", \"left\", \"right\", \"bottom\", \"top\", \"inside\") legend.position.inside numeric vector length two setting placement legends \"inside\" position. legend.direction layout items legends (\"horizontal\" \"vertical\") legend.byrow whether legend-matrix filled columns (FALSE, default) rows (TRUE). legend.justification anchor point positioning legend inside plot (\"center\" two-element numeric vector) justification according plot area positioned outside plot legend.justification.top, legend.justification.bottom, legend.justification.left, legend.justification.right, legend.justification.inside legend.justification specified per legend.position option. legend.location Relative placement legends outside plot string. Can \"panel\" (default) align legends panels \"plot\" align legends plot whole. legend.box arrangement multiple legends (\"horizontal\" \"vertical\") legend.box.just justification legend within overall bounding box, multiple legends (\"top\", \"bottom\", \"left\", \"right\") legend.box.margin margins around full legend area, specified using margin() legend.box.background background legend area (element_rect(); inherits rect) legend.box.spacing spacing plotting area legend box (unit) panel.background background plotting area, drawn underneath plot (element_rect(); inherits rect) panel.border border around plotting area, drawn top plot covers tick marks grid lines. used fill = NA (element_rect(); inherits rect) panel.spacing, panel.spacing.x, panel.spacing.y spacing facet panels (unit). panel.spacing.x & panel.spacing.y inherit panel.spacing can specified separately. panel.grid, panel.grid.major, panel.grid.minor, panel.grid.major.x, panel.grid.major.y, panel.grid.minor.x, panel.grid.minor.y grid lines (element_line()). Specify major grid lines, minor grid lines separately (using panel.grid.major panel.grid.minor) individually axis (using panel.grid.major.x, panel.grid.minor.x, panel.grid.major.y, panel.grid.minor.y). Y axis grid lines horizontal x axis grid lines vertical. panel.grid.*.* inherits panel.grid.* inherits panel.grid, turn inherits line panel.ontop option place panel (background, gridlines) data layers (logical). Usually used transparent blank panel.background. plot.background background entire plot (element_rect(); inherits rect) plot.title plot title (text appearance) (element_text(); inherits title) left-aligned default plot.title.position, plot.caption.position Alignment plot title/subtitle caption. setting plot.title.position applies title subtitle. value \"panel\" (default) means titles /caption aligned plot panels. value \"plot\" means titles /caption aligned entire plot (minus space margins plot tag). plot.subtitle plot subtitle (text appearance) (element_text(); inherits title) left-aligned default plot.caption caption plot (text appearance) (element_text(); inherits title) right-aligned default plot.tag upper-left label identify plot (text appearance) (element_text(); inherits title) left-aligned default plot.tag.position position tag string (\"topleft\", \"top\", \"topright\", \"left\", \"right\", \"bottomleft\", \"bottom\", \"bottomright\") coordinate. coordinate, can numeric vector length 2 set x,y-coordinate relative whole plot. coordinate option unavailable plot.tag.location = \"margin\". plot.tag.location placement tag string, one \"panel\", \"plot\" \"margin\". Respectively, place tag inside panel space, anywhere plot whole, margin around panel space. plot.margin margin around entire plot (unit sizes top, right, bottom, left margins) strip.background, strip.background.x, strip.background.y background facet labels (element_rect(); inherits rect). Horizontal facet background (strip.background.x) & vertical facet background (strip.background.y) inherit strip.background can specified separately strip.clip strip background edges strip labels clipped extend strip background? Options \"\" clip, \"\" disable clipping \"inherit\" (default) take clipping setting parent viewport. strip.placement placement strip respect axes, either \"inside\" \"outside\". important axes strips side plot. strip.text, strip.text.x, strip.text.y, strip.text.x.top, strip.text.x.bottom, strip.text.y.left, strip.text.y.right facet labels (element_text(); inherits text). Horizontal facet labels (strip.text.x) & vertical facet labels (strip.text.y) inherit strip.text can specified separately. Facet strips dedicated position-dependent theme elements (strip.text.x.top, strip.text.x.bottom, strip.text.y.left, strip.text.y.right) inherit strip.text.x strip.text.y, respectively. consequence, theme stylings need applied position-dependent elements rather parent elements strip.switch.pad.grid space strips axes strips switched (unit) strip.switch.pad.wrap space strips axes strips switched (unit) complete set TRUE complete theme, one returned theme_grey(). Complete themes behave differently added ggplot object. Also, setting complete = TRUE elements set inherit blank elements. validate TRUE run validate_element(), FALSE bypass checks.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_theme.html","id":"theme-inheritance","dir":"Reference","previous_headings":"","what":"Theme inheritance","title":"Plot default theme — scheme_theme","text":"Theme elements inherit properties theme elements hierarchically. example, axis.title.x.bottom inherits axis.title.x inherits axis.title, turn inherits text. text elements inherit directly indirectly text; lines inherit line, rectangular objects inherit rect. means can modify appearance multiple elements setting single high-level component. Learn setting aesthetics vignette(\"ggplot2-specs\").","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/scheme_theme.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot default theme — scheme_theme","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 8) ggheatmap(small_mat) + scheme_theme(plot.background = element_rect(fill = \"red\")) #> → heatmap built with `geom_tile()` # `scheme_theme()` serves as the default theme and will always be # overridden by any `theme()` settings applied directly to the plot ggheatmap(small_mat) + theme(plot.background = element_rect(fill = \"blue\")) + scheme_theme(plot.background = element_rect(fill = \"red\")) #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-LayoutProto-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Print Layout object — show,LayoutProto-method","title":"Print Layout object — show,LayoutProto-method","text":"Print Layout object","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-LayoutProto-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print Layout object — show,LayoutProto-method","text":"","code":"# S4 method for class 'LayoutProto' show(object)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-LayoutProto-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print Layout object — show,LayoutProto-method","text":"object quad_layout()/ggheatmap() stack_layout() object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-LayoutProto-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print Layout object — show,LayoutProto-method","text":"input invisiblely.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-ggalign_plot-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Show ggalign_plot information — show,ggalign_plot-method","title":"Show ggalign_plot information — show,ggalign_plot-method","text":"Show ggalign_plot information","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-ggalign_plot-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show ggalign_plot information — show,ggalign_plot-method","text":"","code":"# S4 method for class 'ggalign_plot' show(object)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-ggalign_plot-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show ggalign_plot information — show,ggalign_plot-method","text":"object ggalign_plot object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/show-ggalign_plot-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show ggalign_plot information — show,ggalign_plot-method","text":"input invisiblely.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_cross.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange plots crosswise horizontally or vertically — stack_cross","title":"Arrange plots crosswise horizontally or vertically — stack_cross","text":"stack_cross function derived stack_discrete() allows different layout ordering indices within single layout. Two aliases provided convenience: stack_crossv: special case stack_cross sets direction = \"v\" vertical alignment. stack_crossh: special case stack_cross sets direction = \"h\" horizontal alignment.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_cross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange plots crosswise horizontally or vertically — stack_cross","text":"","code":"stack_cross(direction, data = NULL, ..., theme = NULL, sizes = NA) stack_crossv(data = NULL, ...) stack_crossh(data = NULL, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_cross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange plots crosswise horizontally or vertically — stack_cross","text":"direction string indicating direction stack layout, either \"h\"(horizontal) \"v\"(vertical). data Default dataset use layout. specified, must supplied plot added layout, fortify_matrix() used convert data matrix. ... Additional arguments passed fortify_matrix(). theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. sizes numeric value unit object. used quad_layout() annotation, must length 1. used stack_layout() nested quad_layout(), length 3, specifying relative heights (direction = \"h\") widths (direction = \"v\") applied layout.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange plots horizontally or vertically — stack_layout","title":"Arrange plots horizontally or vertically — stack_layout","text":"limits provided, continuous variable required aligned direction specified (stack_continuous). Otherwise, discrete variable required aligned (stack_discrete). Several aliases provided convenience: stack_vertical: special case stack_layout sets direction = \"v\". stack_horizontal: special case stack_layout sets direction = \"h\". stack_discretev: special case stack_discrete sets direction = \"v\". stack_discreteh: special case stack_discrete sets direction = \"h\". stack_continuousv(): special case stack_free sets direction = \"v\". stack_continuoush(): special case stack_free sets direction = \"h\". historical reasons, following aliases available: stack_align alias stack_discrete. stack_alignv alias stack_discretev. stack_alignh alias stack_discreteh. stack_free alias stack_continuous. stack_freev alias stack_continuousv. stack_freeh alias stack_continuoush.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange plots horizontally or vertically — stack_layout","text":"","code":"stack_layout( direction, data = NULL, ..., theme = NULL, sizes = NA, limits = waiver() ) stack_horizontal(data = NULL, ..., limits = waiver()) stack_vertical(data = NULL, ..., limits = waiver()) stack_discrete(direction, data = NULL, ..., theme = NULL, sizes = NA) stack_discretev(data = NULL, ...) stack_discreteh(data = NULL, ...) stack_continuous( direction, data = NULL, ..., limits = NULL, theme = NULL, sizes = NA ) stack_continuousv(data = NULL, ...) stack_continuoush(data = NULL, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange plots horizontally or vertically — stack_layout","text":"direction string indicating direction stack layout, either \"h\"(horizontal) \"v\"(vertical). data Default dataset use layout. specified, must supplied plot added layout: limits provided, fortify_matrix() used get matrix. limits specified, fortify_data_frame() used get data frame. Note data matrix, automatically converted long-formatted data frame, differs ggplot2's behavior. ... Additional arguments passed fortify_data_frame() fortify_matrix(). theme theme() object used customize various elements layout, including guides, title, subtitle, caption, margins, panel.border, background. default, theme inherit parent layout. also controls panel spacing plots layout. sizes numeric value unit object. used quad_layout() annotation, must length 1. used stack_layout() nested quad_layout(), length 3, specifying relative heights (direction = \"h\") widths (direction = \"v\") applied layout. limits continuous_limits() object specifying left/lower limit right/upper limit scale. Used align continuous axis.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange plots horizontally or vertically — stack_layout","text":"StackLayout object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange plots horizontally or vertically — stack_layout","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7L) stack_horizontal(small_mat) + align_dendro() # this is the same with: stack_discrete(\"h\", small_mat) + align_dendro() stack_discreteh(small_mat) + align_dendro() # For vertical layout: stack_vertical(small_mat) + align_dendro()"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_switch.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine the active context of stack layout — stack_switch","title":"Determine the active context of stack layout — stack_switch","text":"stack_active alias stack_switch(), sets = NULL default.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_switch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the active context of stack layout — stack_switch","text":"","code":"stack_switch(sizes = NULL, what = waiver(), ...) stack_active(sizes = NULL, ...)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_switch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the active context of stack layout — stack_switch","text":"sizes numeric value unit object. used quad_layout() annotation, must length 1. used stack_layout() nested quad_layout(), length 3, specifying relative heights (direction = \"h\") widths (direction = \"v\") applied layout. get activated stack layout? single number string plot elements layout. NULL, remove active context, useful active context quad_layout() object, align_*() added quad_layout(). removing active context, can add align_*() stack_layout(). ... dots future extensions must empty.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_switch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the active context of stack layout — stack_switch","text":"stack_switch object can added stack_layout().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/stack_switch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine the active context of stack layout — stack_switch","text":"","code":"stack_discrete(\"h\", matrix(1:9, nrow = 3L)) + ggheatmap() + # ggheamtap will set the active context, directing following addition # into the heatmap plot area. To remove the heatmap active context, # we can use `stack_active()` which will direct subsequent addition into # the stack stack_active() + # here we add a dendrogram to the stack. align_dendro() #> → heatmap built with `geom_tile()`"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/theme_no_axes.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove axis elements — theme_no_axes","title":"Remove axis elements — theme_no_axes","text":"Remove axis elements","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/theme_no_axes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove axis elements — theme_no_axes","text":"","code":"theme_no_axes( axes = \"xy\", text = TRUE, ticks = TRUE, title = TRUE, line = FALSE )"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/theme_no_axes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove axis elements — theme_no_axes","text":"axes axes elements removed? string containing one \"t\", \"l\", \"b\", \"r\", \"x\", \"y\". text TRUE, remove axis labels. ticks TRUE, remove axis ticks. title TRUE, remove axis title. line TRUE, remove axis line.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/theme_no_axes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove axis elements — theme_no_axes","text":"theme() object.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/theme_no_axes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove axis elements — theme_no_axes","text":"","code":"p <- ggplot() + geom_point(aes(x = wt, y = qsec), data = mtcars) p + theme_no_axes() p + theme_no_axes(\"b\") p + theme_no_axes(\"l\")"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.MAF.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert the shape of a MAF for fortify method — tune.MAF","title":"Convert the shape of a MAF for fortify method — tune.MAF","text":"Convert shape MAF fortify method","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.MAF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert the shape of a MAF for fortify method — tune.MAF","text":"","code":"# S3 method for class 'MAF' tune(data, shape = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.MAF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert the shape of a MAF for fortify method — tune.MAF","text":"data MAF object. shape used currently.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.html","id":null,"dir":"Reference","previous_headings":"","what":"Change the shape of the input object — tune","title":"Change the shape of the input object — tune","text":"Change shape input object","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change the shape of the input object — tune","text":"","code":"tune(data, shape = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change the shape of the input object — tune","text":"data R object. shape Usually NULL string, specifying new shape object. Refer detailed method allowed values.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Change the shape of the input object — tune","text":"cases, fortify_matrix() fortify_data_frame() provide full support transforming objects. However, objects may require two completely different approaches fortified. tune function acts helper create new class tailored objects.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.list.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert the shape of a list for fortify method — tune.list","title":"Convert the shape of a list for fortify method — tune.list","text":"Convert shape list fortify method","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert the shape of a list for fortify method — tune.list","text":"","code":"# S3 method for class 'list' tune(data, shape = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert the shape of a list for fortify method — tune.list","text":"data list shape used currently.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert the shape of a matrix for fortify method — tune.matrix","title":"Convert the shape of a matrix for fortify method — tune.matrix","text":"Convert shape matrix fortify method","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert the shape of a matrix for fortify method — tune.matrix","text":"","code":"# S3 method for class 'matrix' tune(data, shape = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/tune.matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert the shape of a matrix for fortify method — tune.matrix","text":"data matrix. shape used currently.","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify operated Context in quad_layout() — with_quad","title":"Modify operated Context in quad_layout() — with_quad","text":"with_quad() function modifies application context elements ggheatmap()/quad_layout(). controls objects like themes, scales, plot modifications apply specific annotation stacks main plot without altering currently active layout plot.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify operated Context in quad_layout() — with_quad","text":"","code":"with_quad(x, position = waiver(), main = NULL)"},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify operated Context in quad_layout() — with_quad","text":"x object can added ggplot, including schemes. See scheme_align(), scheme_data(), scheme_theme() position string specifying one positions- \"t\", \"l\", \"b\", \"r\"- indicate annotation stack context x. NULL, change operated context quad_layout() . default behaivours, see details section. main single boolean value indicating whether x apply main plot, used position NULL. default, position waiver() active context quad_layout() annotation stack active context stack_layout() , main set TRUE; otherwise, defaults FALSE.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify operated Context in quad_layout() — with_quad","text":"original object added attribute sets specified context.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Modify operated Context in quad_layout() — with_quad","text":"Default Behavior adding object wrapped with_quad(): quad_layout() object: ggheatmap()/quad_layout() active annotation stack, objects added via + - operate normally without with_quad(). active annotation stack set, with_quad() ensures applied object also modifies: main plot (default). Opposite annotation stacks using -. stack_layout() object: active layout stack_layout() : - operator apply changes plots along stack_layout(), means stack layout horizontal, - operator also add element left right annotation, stack layout vertical, - operator also add element top bottom annotation. + operator anything special. active layout nested ggheatmap()/quad_layout(), +/- operator applies elements nested layout, following principles ggheatmap()/quad_layout().","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/reference/with_quad.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify operated Context in quad_layout() — with_quad","text":"","code":"set.seed(123) small_mat <- matrix(rnorm(56), nrow = 7) # By wrapping object with `with_quad()`, the `+` operator will apply the # object not only to the active plot in the annotation stack, but also to # the main plot unless specified by `main` argument otherwise. ggheatmap(small_mat) + # initialize the left annotation anno_left(size = 0.2) + align_dendro() + # apply the object not only to the active plot in the annotation stack, # but also to the main plot with_quad(theme(plot.background = element_rect(fill = \"red\"))) #> → heatmap built with `geom_tile()` # the `-` operator will apply changes not only to the active annotation # stack but also to the opposite one (i.e., bottom if top is active, and # vice versa). The same principle applies to the left and right annotation. ggheatmap(small_mat) + anno_left(size = 0.2) + align_dendro(aes(color = branch), k = 3L) + # Change the active layout to the left annotation anno_top(size = 0.2) + align_dendro(aes(color = branch), k = 3L) + anno_bottom(size = 0.2) + align_dendro(aes(color = branch), k = 3L) - # Modify the color scale of all plots in the bottom and the opposite # annotation, in this way, the `main` argument by default would be `TRUE` with_quad(scale_color_brewer(palette = \"Dark2\", name = \"Top and bottom\")) #> → heatmap built with `geom_tile()` # When the `position` argument is manually set, the # default value of the `main` argument will be `FALSE`. ggheatmap(small_mat) + anno_left(size = 0.2) + align_dendro(aes(color = branch), k = 3L) + anno_top(size = 0.2) + align_dendro(aes(color = branch), k = 3L) + anno_bottom(size = 0.2) + align_dendro(aes(color = branch), k = 3L) - # Modify the background of all plots in the left and top annotation with_quad(theme(plot.background = element_rect(fill = \"red\")), \"tl\") #> → heatmap built with `geom_tile()`"},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"breaking-changes-development-version","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"ggalign (development version)","text":"Now, *_free() layouts removed, layout splitted two type: align discrete continous vairables.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"new-features-development-version","dir":"Changelog","previous_headings":"","what":"New features","title":"ggalign (development version)","text":"new helper function memo_order() reorder oncoplot samples. new geom_subrect() geom_subtile() subdivide rectangles shared borders grid. new cross_link function reset layout ordering index layout panel group, add plot connect selected observations. new cross_mark function reset layout ordering index layout panel group, add plot annotate observations. new pair_links() function create pairs observation groups. new mark_draw(), mark_line(), mark_tetragon() define links connect marked observations. new link_draw(), link_line(), link_tetragon() define links connect pair observations new ggmark() add plot annotate selected observations. new element_vec() functions apply function vectorized fields theme element object. new no_expansion() function remove scale expansion. new layout circle_layout() arrange plot circular. new raster_magick() function post-processing image raster magick package added. new fortify_matrix.GISTIC() method GISTIC object maftools package (#24). + operator now respect with_quad(). new ggalign_attr_set() ggalign_attr_get() basic operations attached attribute. new geom_draw() function draw ggplot2 layer customized draw function.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"bug-fixes-development-version","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"ggalign (development version)","text":"fix breaks labels work well discrete scale (#30, #32) fix wrong results fortify_matrix.MAF() method","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"improvements-development-version","dir":"Changelog","previous_headings":"","what":"Improvements","title":"ggalign (development version)","text":"Now, with_quad() wraps object list class with_quad. approach offers greater flexibility defining actions associated with_quad, allowing customizable behavior (#26, @Yunuuuu). Now, panel reordered initializing layout parameters, don’t need reorder panel drawing. free_gg, align new cross_link objects collapsed one class ggalign_plot","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"ggalign-005","dir":"Changelog","previous_headings":"","what":"ggalign 0.0.5","title":"ggalign 0.0.5","text":"CRAN release: 2024-11-14","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"breaking-changes-0-0-5","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"ggalign 0.0.5","text":"direction argument stack_layout()/ggstack() soft-deprecated now, user must provide manually. set_context, order, name arguments align_*() ggheatmap() soft-deprecated, advised use active argument. guides, free_guides, free_spaces, free_labs, plot_data arguments align_*() ggheatmap() deprecated, advised use scheme_align function instead. theme argument align_*() ggheatmap() deprecated, advised use plot_theme function. argument stack_active() soft-deprecated, user advised use stack_switch() change active plot . align_panel()/ggpanel() deprecated, user advised use ggalign(data = NULL) instead.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"new-features-0-0-5","dir":"Changelog","previous_headings":"","what":"New features","title":"ggalign 0.0.5","text":"new quad_layout() create layout allowing free alignment. new quad_alignv(), quad_alignh(), quad_free()/ggside(), quad_alignb() alias quad_layout(). stack_layout() now gains type argument control whether layout align observations. new ggoncoplot() function draw oncoprint. new ggfree() function add ggplot layout. new fortify_matrix() function convert objects matrix, add fortify_matrix() method MAF object. new fortify_data_frame() function convert objects data frame. now, special attribute ggalign can used pass additional informations across building process, new function ggalign_attr() can used extract data attribute. new plot_theme() function control default theme plot layout. new plot_data() function control data transformation plot layout. new scheme_align() function control specifications plot layout. new with_quad() function control - operator context. new quad_init() function initialize annotation self-provided data. new stack_switch() quad_switch() switch active plots stack_layout() quad_layout(). new anno_top(), anno_left(), anno_bottom() anno_right() alias add annotation quad_layout(). align_dendro() gain new argument cutree customize process tree cutting. reorder_dendrogram argument align_dendro() function now can accept function reorder tree. new layer_order() function change ggplot2 layer adding order. new theme_no_axes() function remove axis elements. new geom_pie() function draw pie charts.","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"bug-fixes-0-0-5","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"ggalign 0.0.5","text":"fix bug apply free_border alignpatches object. fix bug provide function distance argument align_dendro() fix bug provide hclust dendrogram method argument align_dendro() fix bug coord_ggalign() discrete scale","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"improvements-0-0-5","dir":"Changelog","previous_headings":"","what":"Improvements","title":"ggalign 0.0.5","text":"merge function implemented vctrs performance large matrix (> 20000 cells), automatically use geom_raster() {data.table} now removed dependency","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"ggalign-004","dir":"Changelog","previous_headings":"","what":"ggalign 0.0.4","title":"ggalign 0.0.4","text":"CRAN release: 2024-10-12 layout_heatmap()/ggheatmap() arguments width/height renamed .width/.height helps avoid conflicts arguments geom_tile(). nestet alignpatches theme default inherit parent alignpatches new layout_title() function, now layout_annotation() control layout theme add ggrastr::rasterize method ggheatmap() ggstack() set_context argument align_dendro() now depends plot_dendrogram default align_dendro() gain new argument reorder_dendrogram control whether reorder generated dendrogram based mean values. align_reorder() now splitted two function align_order() align_reorder() dendrogram_data() gain new argument reorder_branches control whether reorder input leaf_braches based tree. align_dendro() gain new argument merge_dendrogram control whether dendrograms multiple groups merged dendrogram height axis automatically reversed bottom left annotation stack heatmap fill color scale now default use scale_fill_gradient2(low = \"blue\", high = \"red\") continuous values. Coord used set limits instead Scale free_* arguments now accept argument corresponding free_* functions. new theme_ggalign() function default theme ggalign package export option ggalign.default_theme allow user change global default theme new free_guide() function, override layout guides argument single plot geom_draw() now utilize patch() function convert objects grob internal changes: vectors operated vctrs package stack_layout(): gain sizes argument control relative sizes stack align_()*: now order argument control plot area. align_reorder() now can accept ordering character names. export order2() function align_reorder(): fun argument renamed order argument, can now accept ordering integer index directly fun align_reorder() now can return statistics can handled order2() fix ggheatmap() order work put stack layout method hclust2() can now return objects can coerced hclust, can provide object directly method. hclust2() now can accept distance = NULL hmanno(), stack_active(), align_*() functions gain new argument theme control theme plot. new layout_annotation() layout_theme() modify layout components borders argument free_space() renamed spaces {tibble} now removed dependency align_plots() now can accept gList, function, recordedplot, trellis, pheatmap, Heatmap, HeatmapAnnotation, HeatmapList, added alignpatch method objects. add patch method gList, function, recordedplot, trellis, pheatmap, Heatmap, HeatmapAnnotation, HeatmapList fix bug wrap() function duplicated names gtable cause grobs missing new free_vp() function customize viewport aligning. StackLayout HeatmapLayout methods collapsed one method Layout class New Patch class, now can extend alignment process object customize building process ggproto. fix missing variable labs free_space method PatchAlignpatches","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"ggalign-003","dir":"Changelog","previous_headings":"","what":"ggalign 0.0.3","title":"ggalign 0.0.3","text":"CRAN release: 2024-09-15 Add package logo new inset() function add package quotes DESCRIPTION add return value docs exported function methods","code":""},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"ggalign-002","dir":"Changelog","previous_headings":"","what":"ggalign 0.0.2","title":"ggalign 0.0.2","text":"omit redudnant description add single quote package name","code":""},{"path":[]},{"path":"https://yunuuuu.github.io/ggalign/dev/news/index.html","id":"features-0-0-1","dir":"Changelog","previous_headings":"","what":"Features","title":"ggalign 0.0.1","text":"ggalign pacakge provides two layout arrange ggplot objects: heatmap_layout()/ggheatmap(): Arrange ggplot Heatmap layout. See vignette(\"heatmap-layout\") details. stack_layout()/ggstack(): Arrange ggplot vertically horizontally. See vignette(\"stack-layout\") details. customize layouts, offer following functions: align_group(): Group layout axis panel group variable. align_kmeans(): Group layout axis panel kmeans align_reorder(): Reorders layout observations based weights summary statistics. align_dendro(): Reorder Group layout based hierarchical clustering detailed instructions customizing layouts, see vignette: vignette(\"layout-customize\"). Additionally, plots can added layout following functions: align_gg()/ggalign(): Create ggplot object customized data. align_panel()/ggpanel(): Create ggplot object layout panel data. information adding plots, refer vignette: vignette(\"layout-plot\").","code":""}]