SetDatExpr change when checking for goodgenes (517ee01c) · Commits · github_fork / HdWGCNA

R/getters_and_setters.R

+8 −5

Original line number	Diff line number	Diff line
		@@ -222,18 +222,20 @@ SetDatExpr <- function(
		)[genes_use,cells]
		)


		# transpose data
		datExpr <- as.data.frame(t(datExpr))

		# only get good genes:
		if(is.null(multi.group.by)){
		gene_list = genes_use[WGCNA::goodGenes(datExpr, ...)]
		datExpr <- datExpr[,gene_list]
		}
		# if(is.null(multi.group.by)){
		# gene_list = genes_use[WGCNA::goodGenes(datExpr, ...)]
		# datExpr <- datExpr[,gene_list]
		# }

		if(return_seurat){

		gene_list <- genes_use[WGCNA::goodGenes(datExpr, ...)]
		datExpr <- datExpr[,gene_list]

		# update the WGCNA gene list:
		seurat_obj <- SetWGCNAGenes(seurat_obj, gene_list, wgcna_name)

		@@ -1093,6 +1095,7 @@ GetModulePreservation <- function(seurat_obj, mod_name, wgcna_name=NULL){
		ResetModuleNames <- function(
		seurat_obj,
		new_name = "M",
		reset_levels = FALSE,
		wgcna_name=NULL
		){

+1 −1

Original line number	Diff line number	Diff line
		@@ -510,7 +510,7 @@ ModuleFeaturePlot<- function(
		# use all modules except gray if not specified by the user
		modules <- GetModules(seurat_obj, wgcna_name)
		if(is.null(module_names)){
		module_names <- colnames(MEs)
		module_names <- levels(modules$module)
		module_names <- module_names[module_names != 'grey']
		}