bug fixes (0cea8565) · Commits · github_fork / Plot1cell

DESCRIPTION

+4 −2

+1 −1

Original line number	Diff line number	Diff line
		@@ -83,7 +83,7 @@ label1<-gene_highlight
		if(is.null(label1)){
		label1=rownames(data_plot)
		}
		ht_opt$message = FALSE
		ComplexHeatmap::ht_opt$message = FALSE
		ht<- Heatmap(data_plot,name = "mat", cluster_rows = F, cluster_columns = F,
		column_title = NULL,col = col_fun, row_title = NULL,
		cluster_row_slices = FALSE, cluster_column_slices = FALSE,

+17 −2

Original line number	Diff line number	Diff line
		@@ -28,6 +28,9 @@ complex_vlnplot_single <- function(
		pt.size=0.1,
		split.by=NULL
		){
		if(length(feature)>1){
		stop("Only one gene is allowed in this method. Please use complex_vlnplot_multiple if you want to plot multiple genes.")
		}
		if(is.null(celltypes)){
		celltypes = levels(seu_obj)
		}
		@@ -140,7 +143,17 @@ complex_vlnplot_single <- function(
		stop("This function does not support spliting multiple groups. Plots will look too messy! Please select one group only in the 'groups' parameter if you want to use 'split.by'.")
		}
		if(length(celltypes)==1){
		gene_count<-melt(gene_count[,c(feature, groups)], measure.vars = groups)
		all_levels<-list()
		for(i in 1:length(groups)){
		if (is.null(levels(seu_obj@meta.data[,groups[i]]))){
		seu_obj@meta.data[,groups[i]] <-factor(seu_obj@meta.data[,groups[i]], levels = names(table(seu_obj@meta.data[,groups[i]])))
		}
		group_level<-levels(seu_obj@meta.data[,groups[i]])
		all_levels[[i]]<-group_level
		}
		all_levels<-as.character(unlist(all_levels))
		gene_count<-reshape2::melt(gene_count[,c(feature, groups)], measure.vars = groups)
		gene_count$value<-factor(gene_count$value, levels = all_levels)
		p<-ggplot(gene_count, aes_string(x="value", y=feature, fill="value"))+
		geom_violin(scale = 'width', adjust = 1, trim = TRUE, size=0.3, alpha=0.5, color="pink")+
		xlab("") + ylab("") + ggtitle(feature) +
		@@ -191,3 +204,5 @@ complex_vlnplot_single <- function(
		}
		}
		}