update (89dfaf48) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+16 −15

Original line number	Diff line number	Diff line
		@@ -163,8 +163,8 @@ volcano_plot <- function(
		top_gene_number = 10,
		fold_change = 1.5,
		p_value = 0.05,
		special.gene = NULL,
		special.label = "special",
		special_gene = NULL,
		special_label = "special",
		show_p = TRUE,
		show_fc = TRUE,
		show_gene_number = TRUE,
		@@ -238,49 +238,49 @@ volcano_plot <- function(
		gene_name %in% top.genes$down,
		label_down := gene_name
		][
		gene_name %in% special.gene,
		gene_name %in% special_gene,
		label_special := gene_name
		]

		if(!is.null(special.gene)){
		special.gene <- special.gene %>% .[. %in% dt$gene_name]
		if(!is.null(special_gene)){
		special_gene <- special_gene %>% .[. %in% dt$gene_name]

		dt[
		label_special %in% special.gene,
		color := special.label
		label_special %in% special_gene,
		color := special_label
		]
		}

		if(is.null(special.gene)){
		if(is.null(special_gene)){
		label_all <- c("Down","Not significant","Up")
		color_all <- c(color_down,color_ns,color_up)
		}else{
		label_all <- c("Down","Not significant",special.label,"Up")
		color_all <- c(color_down,color_ns,color_special,color_up)
		label_all <- c(special_label,"Down","Not significant","Up")
		color_all <- c(color_special,color_down,color_ns,color_up)
		}

		plot <- ggplot() +
		geom_point(
		data = dt[color == "not_sig"],
		aes(log2FC,log10P,color = color),
		aes(log2FC,log10P,color = color_ns),
		size = 0.8,
		show.legend = show_legend
		) +
		geom_point(
		data = dt[color == "up"],
		aes(log2FC,log10P,color = color),
		aes(log2FC,log10P,color = color_up),
		size = 0.8,
		show.legend = show_legend
		) +
		geom_point(
		data = dt[color == "down"],
		aes(log2FC,log10P,color = color),
		aes(log2FC,log10P,color = color_down),
		size = 0.8,
		show.legend = show_legend
		) +
		geom_point(
		data = dt[color == special.label],
		aes(log2FC,log10P,color = color),
		data = dt[color == special_label],
		aes(log2FC,log10P,color = color_special),
		size = 0.8,
		show.legend = show_legend
		) +
		@@ -451,6 +451,7 @@ volcano_plot <- function(
		plot
		}


		simple_ego <- function(
		.data,
		regulation,

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