Merge branch 'master' into install

saeyslab · Aug 28, 2024 · 157b0ce · 157b0ce
2 parents c44b091 + 7bda2d8
commit 157b0ce
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Showing 6 changed files with 14 additions and 11 deletions.
diff --git a/R/supporting_functions.R b/R/supporting_functions.R
@@ -197,7 +197,7 @@ convert_alias_to_symbols = function(aliases, organism, verbose = TRUE){
 #' @description \code{alias_to_symbol_seurat} Convert aliases to official gene symbols in a Seurat Object. Makes use of `convert_alias_to_symbols`
 #' @usage alias_to_symbol_seurat(seurat_obj, organism)
 #'
-#' @param seurat_obj Seurat object
+#' @param seurat_obj Seurat object, v4 or below. For Seurat v5, a warning is thrown and the same object will be returned.
 #' @param organism Is Seurat object data from "mouse" or "human"
 #'
 #' @return Seurat object
@@ -219,13 +219,14 @@ alias_to_symbol_seurat = function(seurat_obj, organism) {
 
   # Stop if obj_version is seurat v5
   if (obj_version >= 5){
-    stop("This function is not supported for Seurat v5 objects. Consider using `convert_alias_to_symbols` on your original expression matrix and creating a new Seurat object instead.
+    warning("This function is not supported for Seurat v5 objects, so the same object will be returned. Consider using `convert_alias_to_symbols` on your original expression matrix and creating a new Seurat object instead.
          If this is not feasible, consider checking out Seurat.utils::RenameGenesSeurat.")
+
+    return(seurat_obj)
   }
 
   assays <- Assays(seurat_obj)
 
-
   convert_newnames <- function(feature_names, organism, verbose = FALSE) {
       newnames <- convert_alias_to_symbols(feature_names, organism = organism, verbose = verbose)
 

diff --git a/man/alias_to_symbol_seurat.Rd b/man/alias_to_symbol_seurat.Rd
diff --git a/tests/testthat/test-prioritization.R b/tests/testthat/test-prioritization.R
@@ -11,7 +11,7 @@ test_that("Wrapper function for seurat", {
   if (as.numeric(substr(packageVersion("Seurat"), 1, 1)) < 5){
     seurat_obj_test = alias_to_symbol_seurat(seurat_obj_test, "mouse")
   } else if (grepl("^5", packageVersion("Seurat")) & grepl("^5", seurat_obj_test@version)){
-    expect_error(alias_to_symbol_seurat(seurat_obj_test, "mouse"))
+    expect_warning(alias_to_symbol_seurat(seurat_obj_test, "mouse"))
   }
 
   lr_network_filtered <- lr_network %>% filter(from %in% rownames(seurat_obj_test), to %in% rownames(seurat_obj_test))
@@ -138,7 +138,7 @@ test_that("Prioritization scheme works", {
       pct <- pcts[i]
 
       if (grepl("^5", packageVersion("Seurat"))){
-        expect_error(alias_to_symbol_seurat(seurat_obj_test, "mouse"))
+        expect_warning(alias_to_symbol_seurat(seurat_obj_test, "mouse"))
       } else {
         seurat_obj_test <- alias_to_symbol_seurat(seurat_obj_test, "mouse")
       }

diff --git a/tests/testthat/test-symbol_conversion.R b/tests/testthat/test-symbol_conversion.R
@@ -31,15 +31,17 @@ test_that("Seurat alias conversion works", {
   seurat_object_lite = readRDS(url("https://zenodo.org/record/3531889/files/seuratObj_test.rds"))
 
   seurat_object_lite2 = seurat_object_lite %>% alias_to_symbol_seurat(organism = "mouse")
-  testthat::expect_equal(typeof(seurat_object_lite2), "S4")
+  expect_equal(typeof(seurat_object_lite2), "S4")
 
   seurat_object_lite <- UpdateSeuratObject(seurat_object_lite)
 
   if (grepl("^5", packageVersion("Seurat")) & grepl("^5", seurat_object_lite@version)){
-    expect_error(alias_to_symbol_seurat(seurat_object_lite, "mouse"))
+    expect_warning(alias_to_symbol_seurat(seurat_object_lite, "mouse"))
+    same_seurat_obj <- suppressWarnings(alias_to_symbol_seurat(seurat_object_lite, "mouse"))
+    expect_true(all(rownames(seurat_object_lite) == rownames(same_seurat_obj)))
   } else {
     seurat_object_lite2 = seurat_object_lite %>% alias_to_symbol_seurat(organism = "mouse")
-    testthat::expect_equal(typeof(seurat_object_lite2), "S4")
+    expect_equal(typeof(seurat_object_lite2), "S4")
   }
 
 })
diff --git a/vignettes/seurat_steps.Rmd b/vignettes/seurat_steps.Rmd
@@ -416,7 +416,7 @@ DE_table_top_ligands <- lapply(
 DE_table_top_ligands <- DE_table_top_ligands %>%  reduce(., full_join) %>% 
   column_to_rownames("gene") 
 
-vis_ligand_lfc <- as.matrix(DE_table_top_ligands[rev(best_upstream_ligands), ]) 
+vis_ligand_lfc <- as.matrix(DE_table_top_ligands[rev(best_upstream_ligands), , drop = FALSE]) 
 
 p_lfc <- make_threecolor_heatmap_ggplot(vis_ligand_lfc,
                                 "Prioritized ligands", "LFC in Sender",

diff --git a/vignettes/seurat_steps.md b/vignettes/seurat_steps.md
@@ -663,7 +663,7 @@ DE_table_top_ligands <- lapply(
 DE_table_top_ligands <- DE_table_top_ligands %>%  reduce(., full_join) %>% 
   column_to_rownames("gene") 
 
-vis_ligand_lfc <- as.matrix(DE_table_top_ligands[rev(best_upstream_ligands), ]) 
+vis_ligand_lfc <- as.matrix(DE_table_top_ligands[rev(best_upstream_ligands), , drop = FALSE])
 
 p_lfc <- make_threecolor_heatmap_ggplot(vis_ligand_lfc,
                                 "Prioritized ligands", "LFC in Sender",