Fix(integration): generate tiles directly instead of after the fact -…

… lead to issue down the line

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -76,6 +76,6 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
 VignetteBuilder: knitr
-URL: https://patrickcnmartin.github.io/Vesalius/,https://github.com/patrickCNMartin/Vesalius
+URL: https://patrickcnmartin.github.io/Vesalius/, https://github.com/patrickCNMartin/Vesalius, https://wonlab-cs.github.io/Vesalius/
 Config/testthat/edition: 3
 Config/rextendr/version: 0.2.0.9000

R/integration.R

@@ -24,6 +24,8 @@
 #' should be merged with the reference data (see details)
 #' @param labels_reference character - which columns in the reference data assay
 #' should be merged with the mapped data (see details)
+#' @param regenerate_tiles logical - should tiles be regenrated from integrated 
+#' coordinates
 #' @param verbose logical - should progressed message be printed
 #' @details After mapping coordinates from a query onto a reference, vesalius
 #' provides a way to then integrate the assays together. This function will:
@@ -53,6 +55,10 @@ integrate_assays <- function(mapped,
     use_counts = "raw",
     labels_mapped = NULL,
     labels_reference = NULL,
+    regenerate_tiles = TRUE,
+    tensor_resolution = 1,
+    filter_grid = 1,
+    filter_threshold = 1,
     verbose = TRUE) {
     simple_bar(verbose)
     #-------------------------------------------------------------------------#
@@ -92,7 +98,16 @@ integrate_assays <- function(mapped,
         coordinates,
         labels_mapped,
         labels_reference)
-    vesalius_assay <- build_vesalius_assay(coordinates = coordinates, verbose = FALSE)
+    vesalius_assay <- build_vesalius_assay(
+        coordinates = coordinates,
+        verbose = FALSE)
+    if (regenerate_tiles) {
+        vesalius_assay <- generate_tiles(vesalius_assay,
+            tensor_resolution = tensor_resolution,
+            filter_grid = filter_grid,
+            filter_threshold = filter_threshold,
+            verbose = verbose)
+    }
     vesalius_assay <- update_vesalius_assay(vesalius_assay,
         data = integrated$counts,
         slot = "counts",
@@ -128,6 +143,7 @@ integrate_assays <- function(mapped,
     vesalius_assay <- commit_log(vesalius_assay,
       commit,
       "Integrated")
+
     simple_bar(verbose)
     return(vesalius_assay)
 }

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: ~
+url: wonlab-cs.github.io/Vesalius/
 template:
   bootstrap: 5
 

vignettes/vesalius.Rmd

@@ -197,7 +197,7 @@ images.
 p3 <- image_plot(vesalius, dimensions = 1, embedding = "UMAP") +
   labs(title = "Grey UMAP dim 1")
 p4 <- image_plot(vesalius, dimensions = c(1, 2, 3), embedding = "UMAP") +
-  labs(title = "Grey UMAP dim 1, 2, and 3")
+  labs(title = "RGB UMAP dim 1, 2, and 3")
 ```
 
 ```{r out_plot_grey, eval = TRUE, echo = TRUE, fig.width = 10, fig.height = 10}
@@ -387,6 +387,7 @@ vesalius <- generate_embeddings(vesalius,
     filter_threshold = 1,
     filter_grid = 1)
 vesalius <- smooth_image(vesalius, embedding = "PCA", sigma = 5, iter = 10)
+vesalius <- equalize_image(vesalius, sleft = 5, sright = 5)
 vesalius <- segment_image(vesalius, col_resolution = 2)
 vesalius <- isolate_territories(vesalius)
 
@@ -425,14 +426,13 @@ matched <- generate_embeddings(matched,
     dim_reduction = "PCA",
   nfeatures = 200, 
   verbose = FALSE)
-matched <- regularise_image(matched, lambda = 1)
 matched <- smooth_image(matched, sigma = 5, iter = 10)
 matched <- equalize_image(matched, sleft = 5, sright = 5)
 matched <- segment_image(matched,col_resolution = 2)
 ```
 We can then look at the resulting embeddings
 
-```{r map_image_plot, eval = TRUE, echo = TRUE}
+```{r map_image_plot, eval = TRUE, echo = TRUE,fig.width = 12}
 m <- image_plot(vesalius)
 m1 <- image_plot(jitter_ves)
 m2 <- image_plot(matched)
@@ -443,10 +443,11 @@ m + m1 + m2
 
 We can also look at the new territories.
 
-```{r map_territory, eval = TRUE, echo = TRUE}
+```{r map_territory, eval = TRUE, echo = TRUE,fig.width = 12}
 t <- territory_plot(vesalius)
 t1 <- territory_plot(jitter_ves)
 t2 <- territory_plot(matched)
+t + t1 + t2
 ```
 
 ## Integrating data sets
@@ -457,22 +458,23 @@ expression analysis.
 ```{r map_inter, eval = TRUE, echo = TRUE}
 inter <- integrate_assays(matched,
     vesalius)
+
+
 ```
 
 Since this data set now contains an integrated latent space, we can also call
 territories on this object. There is no need to create new embeddings. They are
 provided during integration. 
 
 ```{r inter_territory, eval = TRUE, echo = TRUE}
-inter <- regularise_image(inter, lambda = 1)
 inter <- smooth_image(inter, sigma = 5, iter = 10)
 inter <- equalize_image(inter, sleft = 5, sright = 5)
-inter <- segment_image(col_resolution = 2)
+inter <- segment_image(inter, col_resolution = 2)
 ```
 
 We can view the resulting embeddings and territories.
 
-```{r inter_plot, eval = TRUE, echo = TRUE}
+```{r inter_plot, eval = TRUE, echo = TRUE, fig.width = 9}
 i <- image_plot(inter)
 i1 <- territory_plot(inter)