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vertesy · Jun 5, 2024 · 2cc9940 · 2cc9940
1 parent 288daeb
commit 2cc9940
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/R/Seurat.Utils.R b/R/Seurat.Utils.R
@@ -183,7 +183,7 @@ processSeuratObject <- function(obj, param.list = p, add.meta.fractions = FALSE,
 #' @description Runs a differential gene expression analysis based on specified parameters,
 #' reorders clusters if needed, and optionally saves results. Supports output and plotting configurations.
 #'
-#' @param obj Seurat object, assumed to be pre-configured with necessary data. Default: obj.RG.
+#' @param obj Seurat object, assumed to be pre-configured with necessary data.
 #' @param param.list List of parameters for DE analysis. Default: p.
 #' @param reorder.clusters Logical indicating whether to reorder clusters based on dimension.
 #'        Default: TRUE.
@@ -220,7 +220,7 @@ processSeuratObject <- function(obj, param.list = p, add.meta.fractions = FALSE,
 #'
 #' @export
 
-runDGEA <- function(obj = obj.RG,
+runDGEA <- function(obj,
                     param.list = p,
                     reorder.clusters = TRUE,
                     clean.misc.slot = TRUE,

diff --git a/R/Seurat.Utils.Visualization.R b/R/Seurat.Utils.Visualization.R
@@ -1859,7 +1859,7 @@ qUMAP <- function(
     ...) {
   #
   stopifnot(is(obj) == "Seurat")
-  message("feature: ", feature, "assay: ", assay)
+  message("Feature: ", feature, " | Assay: ", assay)
 
   if (feature %in% colnames(obj@meta.data)) {
     message(paste("...found in @meta.data."))

diff --git a/man/qQC.plots.BrainOrg.Rd b/man/qQC.plots.BrainOrg.Rd