rich text

Project.toml

@@ -12,6 +12,7 @@ SnpArrays = "4e780e97-f5bf-4111-9dc4-b70aaf691b06"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
+CairoMakie = "0.11"
 DataFrames = "1"
 Distributions = "0.25"
 Makie = "0.20"

docs/src/examples/genes.md

@@ -23,7 +23,7 @@ set_theme!(font = "Arial")
 
 gene = "CACNA1G"
 chr, start, stop = GeneticsMakie.findgene(gene, gencode)
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 ranges = [start - 1e5, stop + 1e5]
 rs = GeneticsMakie.plotgenes!(ax, chr, ranges[1], ranges[2], gencode)
@@ -36,7 +36,7 @@ f
 
 We can adjust the height of exons using the `height` keyword argument.
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs = GeneticsMakie.plotgenes!(ax, chr, ranges[1], ranges[2], gencode; height = 0.1)
 GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, ranges[1], ranges[2])
@@ -48,7 +48,7 @@ f
 
 We can change the color of genes and text using the `genecolor` and `textcolor` keyword arguments, respectively.
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs = GeneticsMakie.plotgenes!(ax, chr, ranges[1], ranges[2], gencode; height = 0.1, genecolor = :mediumorchid3, textcolor = :forestgreen)
 GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, ranges[1], ranges[2])
@@ -61,7 +61,7 @@ f
 Alternatively, we can visualize this locus by passing `gene` as a positional argument and 
 `window` as a keyword argument.
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs = GeneticsMakie.plotgenes!(ax, gene, gencode; window = 1e5, height = 0.1, genecolor = :brown3)
 GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, ranges[1], ranges[2])
@@ -74,7 +74,7 @@ f
 There is no limit to the number of genes we can visualize. Below we visualize a larger 
 ± 2 Mb window around `gene`.
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs = GeneticsMakie.plotgenes!(ax, gene, gencode; window = 2e6, height = 0.1)
 GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, start - 2e6, stop + 2e6)
@@ -96,7 +96,7 @@ by certain properties such as those that are protein coding or those that are
 significant in some sort of gene-level association. 
 
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs = GeneticsMakie.plotgenes!(ax, chr, start, (gene, :brown3), gencode; window = 1e5, height = 0.1)
 GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, start - 1e5, start + 1e5)
@@ -107,7 +107,7 @@ f
 ![](../figs/CACNA1G-gene-highlight.png)
 
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs = GeneticsMakie.plotgenes!(ax, chr, start, ([gene, "EPN3"], [:brown3, :forestgreen]), gencode; window = 1e5, height = 0.1)
 GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, start - 1e5, start + 1e5)
@@ -121,7 +121,7 @@ Finally, we can make additional modifications on top of the figure as needed usi
 [__Makie.jl__](https://makie.juliaplots.org/stable/).
 
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs = GeneticsMakie.plotgenes!(ax, chr, start, gencode; window = 1e5, height = 0.1)
 GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, start - 1e5, start + 1e5)

docs/src/examples/gtf.md

@@ -29,7 +29,7 @@ gencode = CSV.read("data/gencode/$(file)", DataFrame; delim = "\t", comment = "#
     GRCh37 genomic coordinates. Make sure to use the matching human genome build when
     visualizing your results. 
 
-The ninth column of a [GTF file](https://uswest.ensembl.org/info/website/upload/gff.html) 
+The ninth column of a [GTF file](https://www.gencodegenes.org/pages/data_format.html) 
 contains rich information about features, so we can parse this column.
 ```julia
 GeneticsMakie.parsegtf!(gencode)

docs/src/examples/gwas.md

@@ -18,7 +18,7 @@ titles = ["Height (Yengo et al. 2018)", "Weight (Yengo et al. 2018)"]
 ```
 
 ```julia
-f = Figure(resolution = (408, 792))
+f = Figure(size = (408, 792))
 axs = [Axis(f[i, 1]) for i in 1:length(titles)]
 for i in eachindex(titles)
     GeneticsMakie.plotgwas!(axs[i], dfs[i])
@@ -55,7 +55,7 @@ f
 We can color even and odd chromosomes with different colors by using the `chromcolors` keyword argument. 
 
 ```julia
-f = Figure(resolution = (408, 792))
+f = Figure(size = (408, 792))
 axs = [Axis(f[i, 1]) for i in 1:length(titles)]
 for i in eachindex(titles)
     GeneticsMakie.plotgwas!(axs[i], dfs[i]; linecolor = nothing, scattercolor = nothing, 
@@ -73,7 +73,7 @@ f
 
 We can then use `GeneticsMakie.plotqq!` to draw QQ plots.
 ```julia
-f = Figure(resolution = (408, 792))
+f = Figure(size = (408, 792))
 axs = [Axis(f[2, i]) for i in 1:length(titles)]
 for i in eachindex(titles)
     GeneticsMakie.plotqq!(axs[i], dfs[i]; ystep = 5)

docs/src/examples/isoforms.md

@@ -19,7 +19,7 @@ isdir("figs") || mkdir("figs")
 set_theme!(font = "Arial")
 
 gene = "NRXN1"
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs, chr, range1, range2 = GeneticsMakie.plotisoforms!(ax, gene, gencode; height = 0.1)
 GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, range1, range2)
@@ -32,7 +32,7 @@ f
 To save some space, we can plot the isoform labels on the left by using the `text` keyword argument. 
 
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs, chr, range1, range2 = GeneticsMakie.plotisoforms!(ax, gene, gencode; height = 0.1, text = :l)
 GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, range1, range2)
@@ -47,7 +47,7 @@ We look at a different gene, _GRIN2A_.
 
 ```julia
 gene = "GRIN2A"
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs, chr, range1, range2 = GeneticsMakie.plotisoforms!(ax, gene, gencode; isoformcolor = :forestgreen, height = 0.1)
 GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, range1, range2)
@@ -60,7 +60,7 @@ f
 We can change the order of isoforms by using the `orderby` keyword argument.
 
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs, chr, range1, range2 = GeneticsMakie.plotisoforms!(ax, gene, gencode; orderby = ["ENST00000675189", "ENST00000463531"], isoformcolor = :forestgreen, height = 0.1)
 GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, range1, range2)
@@ -71,7 +71,7 @@ f
 ![](../figs/GRIN2A-isoform-order.png)
 
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 ax = Axis(f[1, 1])
 rs, chr, range1, range2 = GeneticsMakie.plotisoforms!(ax, gene, gencode; orderby = ["ENST00000675189", "ENST00000463531"], 
     highlight = (["ENST00000675398", "ENST00000562109"], fill(:brown3, 2)), isoformcolor = :forestgreen, height = 0.1)

docs/src/examples/locus.md

@@ -28,7 +28,7 @@ ranges = [start - 1e6, stop + 1e6]
 
 n = length(dfs)
 titles = ["Height (Yengo et al. 2018)", "Weight (Yengo et al. 2018)"]
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 axs = [Axis(f[i, 1]) for i in 1:(n + 1)]
 for i in 1:n
     GeneticsMakie.plotlocus!(axs[i], chr, ranges[1], ranges[2], dfs[i])
@@ -43,7 +43,7 @@ Colorbar(f[1:n, 2], limits = (0, 1), ticks = 0:1:1, height = 20,
     colormap = [:gray60, :red2], label = "LD", ticksize = 0, tickwidth = 0,
     tickalign = 0, ticklabelsize = 6, flip_vertical_label = true,
     labelsize = 6, width = 5, spinewidth = 0.5)
-Label(f[1:n, 0], text = "-log[p]", fontsize = 6, rotation = pi / 2)
+Label(f[1:n, 0], rich("-log", subscript("10"), rich("P", font = :italic)), fontsize = 6, rotation = pi / 2)
 rowgap!(f.layout, 5)
 colgap!(f.layout, 5)
 for i in 1:(n + 1)
@@ -73,7 +73,7 @@ kgp = SnpData("data/1kg/kgp.chr15")
 We can then color variants by LD with the index/sentinel SNP by using the `ld` keyword argument.
 
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 axs = [Axis(f[i, 1]) for i in 1:(n + 1)]
 for i in 1:n
     GeneticsMakie.plotlocus!(axs[i], chr, ranges[1], ranges[2], dfs[i]; ld = kgp)
@@ -88,7 +88,7 @@ Colorbar(f[1:n, 2], limits = (0, 1), ticks = 0:1:1, height = 20,
     colormap = [:gray60, :red2], label = "LD", ticksize = 0, tickwidth = 0,
     tickalign = 0, ticklabelsize = 6, flip_vertical_label = true,
     labelsize = 6, width = 5, spinewidth = 0.5)
-Label(f[1:n, 0], text = "-log[p]", fontsize = 6, rotation = pi / 2)
+Label(f[1:n, 0], rich("-log", subscript("10"), rich("P", font = :italic)), fontsize = 6, rotation = pi / 2)
 rowgap!(f.layout, 5)
 colgap!(f.layout, 5)
 for i in 1:(n + 1)
@@ -103,7 +103,7 @@ f
 We can also color variants by LD with the same SNP by using the `ld` keyword argument.
 
 ```julia
-f = Figure(resolution = (306, 792))
+f = Figure(size = (306, 792))
 axs = [Axis(f[i, 1]) for i in 1:(n + 1)]
 for i in 1:n
     GeneticsMakie.plotlocus!(axs[i], chr, ranges[1], ranges[2], dfs[i]; ld = (kgp, ("15", 89395626)))
@@ -118,7 +118,7 @@ Colorbar(f[1:n, 2], limits = (0, 1), ticks = 0:1:1, height = 20,
     colormap = [:gray60, :red2], label = "LD", ticksize = 0, tickwidth = 0,
     tickalign = 0, ticklabelsize = 6, flip_vertical_label = true,
     labelsize = 6, width = 5, spinewidth = 0.5)
-Label(f[1:n, 0], text = "-log[p]", fontsize = 6, rotation = pi / 2)
+Label(f[1:n, 0], rich("-log", subscript("10"), rich("P", font = :italic)), fontsize = 6, rotation = pi / 2)
 rowgap!(f.layout, 5)
 colgap!(f.layout, 5)
 for i in 1:(n + 1)

src/plotgwas.jl

@@ -55,7 +55,7 @@ function plotgwas!(
     hideydecorations!(ax, label = false, ticklabels = false, ticks = false)
     hidexdecorations!(ax, label = false, ticklabels = false)
     ax.xlabel = "Chromosome"
-    ax.ylabel = "-log[p]"
+    ax.ylabel = rich("-log", subscript("10"), rich("P", font = :italic))
     ax.xticks = ((cumsum(storage.maxpos) + storage.add) / 2, storage.CHR)
     ax.yticks = setticks(ymax)
     ax.xticklabelsize = 6

src/plotqq.jl

@@ -38,8 +38,8 @@ function plotqq!(
     ylims!(ax, 0, ymax)
     hidedecorations!(ax, label = false, ticklabels = false, ticks = false)
     ax.aspect = AxisAspect(1)
-    ax.xlabel = "Expected -log[p]"
-    ax.ylabel = "Observed -log[p]"
+    ax.xlabel = rich("Expected -log", subscript("10"), rich("P", font = :italic))
+    ax.ylabel = rich("Observed -log", subscript("10"), rich("P", font = :italic))
     ax.xticklabelsize = 6
     ax.yticklabelsize = 6
     ax.xlabelsize = 8