modified RNA-seq.R in R (a8315dbf) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+13 −2

Original line number	Diff line number	Diff line
		@@ -298,6 +298,7 @@ de.gene <- function(
		c.volcano <- function(
		.data,
		compare = NULL,
		compare_label = NULL,
		top_gene_number = 10,
		fold_change = 2,
		p_value = 0.05,
		@@ -378,6 +379,9 @@ c.volcano <- function(
		,label_down := fcase(rank %in% 0:top_gene_number & sub_regulation == "down",gene_name)
		][
		,label_special := fcase(gene_name %in% special_gene,gene_name)
		][
		data.table(compare,compare_label),
		on = "compare"
		]

		stat <- merge(
		@@ -438,8 +442,15 @@ c.volcano <- function(
		color = color_special,
		size = point_size,
		show.legend = show_legend
		) +
		)

		if(length(compare_label) != n_compare){
		plot <- plot +
		facet_wrap(~ compare)
		}else{
		plot <- plot +
		facet_wrap(~ compare_label)
		}

		xlimits <- max(abs(min(dt$log2FC)),abs(max(dt$log2FC))) + extend_size