Updated vignette for different versions of Seurat

ctlab · Oct 7, 2024 · 077afd8 · 077afd8
1 parent 2f27248
commit 077afd8
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Showing 3 changed files with 32 additions and 4 deletions.
diff --git a/R/geseca-plot.R b/R/geseca-plot.R
@@ -267,7 +267,9 @@ plotCoregulationProfileSpatial <- function(pathway,
                                            title=NULL,
                                            assay=DefaultAssay(object),
                                            colors=c("darkblue", "lightgrey", "darkred"),
-                                           guide="colourbar", ...) {
+                                           guide="colourbar",
+                                           image.alpha = 0,
+                                           ...) {
     stopifnot(requireNamespace("Seurat"))
     # TODO duplicated code with plotCoregulationProfileReduction
     if (is.list(pathway)) {
@@ -286,6 +288,7 @@ plotCoregulationProfileSpatial <- function(pathway,
                                            title = titles[i],
                                            assay = assay,
                                            colors = colors,
+                                           image.alpha = image.alpha,
                                            ...))
         names(ps) <- names(pathway)
         ps <- unlist(ps, recursive = FALSE)
@@ -296,7 +299,7 @@ plotCoregulationProfileSpatial <- function(pathway,
     obj2 <- addGesecaScores(list(pathway = pathway), object,
                                     assay = assay, scale = TRUE)
     ps <- Seurat::SpatialFeaturePlot(obj2, features = "pathway",
-                                     combine = FALSE, image.alpha = 0, ...)
+                                     combine = FALSE, image.alpha = image.alpha, ...)
     # suppress message of replacing existing color palette
     suppressMessages(ps <- lapply(ps, function(p){
         res <- p + scale_fill_gradientn(limits = c(-3, 3),

diff --git a/vignettes/fgsea-tutorial.Rmd b/vignettes/fgsea-tutorial.Rmd
@@ -175,3 +175,9 @@ bg <- names(exampleRanks)
 foraRes <- fora(genes=fg, universe=bg, pathways=examplePathways)
 head(foraRes)
 ```
+
+## Session info
+
+```{r}
+sessionInfo()
+```
diff --git a/vignettes/geseca-tutorial.Rmd b/vignettes/geseca-tutorial.Rmd
@@ -349,8 +349,20 @@ Finally, let us plot spatial expression of the top four pathways:
 topPathways <- gesecaRes[, pathway] |> head(4)
 titles <- sub("HALLMARK_", "", topPathways)
 
+pt.size.factor <- 1.6
+
+
+# Starting from Seurat version 5.1.0, the scaling method for spatial plots was changed.
+# As mentioned here: https://github.com/satijalab/seurat/issues/9049
+# This code provides a workaround to adapt to the new scaling behavior.
+if (packageVersion("Seurat") >= "5.1.0"){
+    sfactors <- ScaleFactors(obj@images$slice1)
+    pt.size.factor <- 1.5 * sfactors$fiducial / sfactors$hires
+}
+
 ps <- plotCoregulationProfileSpatial(pathways[topPathways], obj,
-                                       title=titles)
+                                     title=titles, 
+                                     pt.size.factor=pt.size.factor)
 cowplot::plot_grid(plotlist=ps, ncol=2)
 ```
 
@@ -363,8 +375,15 @@ is more characteristic to the "normal" tissue region:
 ```{r fig.width=5, fig.height=3.5, out.width="50%"}
 plotCoregulationProfileSpatial(pathways$HALLMARK_OXIDATIVE_PHOSPHORYLATION,
                                obj,
-                               title=sprintf("HALLMARK_OXIDATIVE_PHOSPHORYLATION (pval=%.2g)",
+                               pt.size.factor=pt.size.factor,
+                               title=sprintf("HALLMARK_OXIDATIVE_PHOSPHORYLATION\n(pval=%.2g)",
                                              gesecaRes[
                                                  match("HALLMARK_OXIDATIVE_PHOSPHORYLATION", pathway),
                                                  pval]))
 ```
+
+## Session info
+
+```{r echo=TRUE}
+sessionInfo()
+```