Fixed R CMD Check errors.

enblacar · Aug 20, 2024 · 6bbeaa9 · 6bbeaa9
1 parent 3d7a808
commit 6bbeaa9
Show file tree

Hide file tree

Showing 5 changed files with 16 additions and 11 deletions.
diff --git a/R/do_DotPlot.R b/R/do_DotPlot.R
@@ -18,7 +18,7 @@ do_DotPlot <- function(sample,
                        zscore.data = FALSE,
                        min.cutoff = NA,
                        max.cutoff = NA,
-                       enforce_symmetry = ifelse(base::isTRUE(scale.data), TRUE, FALSE), 
+                       enforce_symmetry = ifelse(base::isTRUE(zscore.data), TRUE, FALSE), 
                        legend.title = NULL,
                        legend.type = "colorbar",
                        legend.position = "bottom",

diff --git a/R/do_RankedExpressionPlot.R b/R/do_RankedExpressionPlot.R
@@ -190,6 +190,17 @@ do_RankedExpressionPlot <- function(sample,
   key_col <- stringr::str_remove_all(key, "_")
   # Obtain the DC embeddings, together with the enrichment scores.
   suppressWarnings({
+    # Workaround parameter depreciation.
+  if (base::isTRUE(utils::packageVersion("Seurat") < "4.9.9")){
+    data <- Seurat::GetAssayData(object = sample,
+                                 assay = assay,
+                                 slot = slot)
+  } else {
+    data <- SeuratObject::LayerData(object = sample,
+                                    assay = assay,
+                                    layer = slot)
+  }
+
   data.use <- sample@reductions[[reduction]]@cell.embeddings %>% 
               as.data.frame() %>% 
               tibble::rownames_to_column(var = "Cell") %>% 
@@ -208,9 +219,7 @@ do_RankedExpressionPlot <- function(sample,
                                     tibble::rownames_to_column(var = "Cell") %>% 
                                     tibble::as_tibble() %>% 
                                     dplyr::select(dplyr::all_of(c("Cell", group.by))) %>% 
-                                    dplyr::left_join(y = {SeuratObject::GetAssayData(sample,
-                                                               assay = assay,
-                                                               slot = slot)[features, , drop = FALSE] %>% 
+                                    dplyr::left_join(y = {data[features, , drop = FALSE] %>% 
                                                           as.data.frame() %>% 
                                                           t() %>% 
                                                           as.data.frame() %>% 

diff --git a/man/do_DotPlot.Rd b/man/do_DotPlot.Rd
diff --git a/man/do_RankedExpressionPlot.Rd b/man/do_RankedExpressionPlot.Rd
diff --git a/man/examples/examples_do_RankedExpressionPlot.R b/man/examples/examples_do_RankedExpressionPlot.R
@@ -9,9 +9,7 @@
     sample <- readRDS(system.file("extdata/seurat_dataset_example.rds", package = "SCpubr"))
 
     # Genes have to be unique.
-    genes <- list("A" = rownames(sample)[1:5],
-                  "B" = rownames(sample)[6:10],
-                  "C" = rownames(sample)[11:15])
+    genes <- rownames(sample)[1:15]
 
 
     # This will query, for the provided components, the expression of the genes