extend the volcano figure (2763e7b3) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+93 −37

Original line number	Diff line number	Diff line
		@@ -158,17 +158,18 @@ de.gene <- function(
		}
		}


		volcano_plot <- function(
		.data,
		top_gene_number = 10,
		fold_change = 1.5,
		p_value = 0.05,
		special.gene = NULL,
		special.label = "special",
		show_p = TRUE,
		show_fc = TRUE,
		show_gene_number = TRUE,
		show_legend = FALSE,
		legend_position = "right",
		sub_gene = NULL,
		sub_id = NULL,
		color_up = "#E64B35",
		@@ -180,7 +181,8 @@ volcano_plot <- function(
		fc_line_type = "dashed",
		p_line_color = "black",
		left_fc_line_color = "black",
		right_fc_line_color = "black"
		right_fc_line_color = "black",
		font = "serif"
		){
		if(is.null(sub_gene)){sub_gene <- .data$gene_name}
		if(is.null(sub_id)){sub_id <- .data$gene_id}
		@@ -244,43 +246,49 @@ volcano_plot <- function(

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

		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)
		}

		plot <- ggplot() +
		geom_point(
		data = dt[color == "not_sig"],
		aes(log2FC,log10P),
		color = color_ns,
		aes(log2FC,log10P,color = color),
		size = 0.8,
		show.legend = show_legend
		) +
		geom_point(
		data = dt[color == "up"],
		aes(log2FC,log10P),
		color = color_up,
		aes(log2FC,log10P,color = color),
		size = 0.8,
		show.legend = show_legend
		) +
		geom_point(
		data = dt[color == "down"],
		aes(log2FC,log10P),
		color = color_down,
		aes(log2FC,log10P,color = color),
		size = 0.8,
		show.legend = show_legend
		) +
		geom_point(
		data = dt[color == "special"],
		aes(log2FC,log10P),
		color = color_special,
		data = dt[color == special.label],
		aes(log2FC,log10P,color = color),
		size = 0.8,
		show.legend = show_legend
		)
		) +
		scale_color_manual(values = color_all, label = label_all)

		if(isFALSE(hyperbola)){
		xlimits <- max(abs(min(dt$log2FC)),abs(max(dt$log2FC)))
		extend_size <- 3
		xlimits <- max(abs(min(dt$log2FC)),abs(max(dt$log2FC))) + extend_size

		if(isFALSE(hyperbola)){
		plot <- plot +
		geom_hline(
		yintercept = -log10(p_value),
		@@ -302,7 +310,17 @@ volcano_plot <- function(
		hyperbola_dt_l <- dt[log2FC < 0,.(log2FC = log2FC * -1, hyperbola_log10P)]
		}

		hyperbola_dt <- rbind(hyperbola_dt_l,hyperbola_dt_r)[hyperbola_log10P > -log10(p_value)]
		hyperbola_extend <- data.table(
		log2FC = c((xlimits * -1):(xlimits * -1 + extend_size),(xlimits - extend_size):xlimits)
		)[
		,hyperbola_log10P := 1/((abs(log2FC)) - log2(fold_change)) - log10(p_value)
		]

		hyperbola_dt <- rbind(
		hyperbola_extend,
		hyperbola_dt_l,
		hyperbola_dt_r
		)[hyperbola_log10P > -log10(p_value)]

		plot <- plot +
		geom_line(
		@@ -320,46 +338,81 @@ volcano_plot <- function(
		data = dt,
		aes(x = log2FC, y = log10P),
		label = dt$label_up,
		max.overlaps = Inf,
		box.padding = 1,
		box.padding = 0.1,
		na.rm = T,
		color = color_up
		color = color_up,
		min.segment.length = 0,
		force = 2,
		force_pull = 2,
		max.overlaps = Inf,
		segment.linetype = 3, #线段类型,1为实线,2-6为不同类型虚线
		segment.color = 'black', #线段颜色
		segment.alpha = 0.5, #线段不透明度
		nudge_x = xlimits - dt$log2FC, #标签x轴起始位置调整
		direction = "y", #按y轴调整标签位置方向，若想水平对齐则为x
		hjust = 0,
		fontface = "italic"
		) +
		geom_text_repel(
		data = dt,
		aes(x = log2FC, y = log10P),
		label = dt$label_down,
		box.padding = 0.1,
		max.overlaps = Inf,
		box.padding = 1,
		na.rm = T,
		color = color_down
		color = color_down,
		min.segment.length = 0,
		force = 2,
		force_pull = 2,
		segment.linetype = 3, #线段类型,1为实线,2-6为不同类型虚线
		segment.color = 'black', #线段颜色
		segment.alpha = 0.5, #线段不透明度
		nudge_x = xlimits * -1 - dt$log2FC, #标签x轴起始位置调整
		direction = "y", #按y轴调整标签位置方向，若想水平对齐则为x
		hjust = 0,
		fontface = "italic"
		) +
		geom_text_repel(
		data = dt,
		aes(x = log2FC, y = log10P),
		label = dt$label_special,
		max.overlaps = Inf,
		box.padding = 1,
		box.padding = 0.1,
		na.rm = T,
		color = color_special
		color = color_special,
		min.segment.length = 0,
		force = 2,
		force_pull = 2,
		max.overlaps = Inf,
		segment.linetype = 3, #线段类型,1为实线,2-6为不同类型虚线
		segment.color = 'black', #线段颜色
		segment.alpha = 0.5, #线段不透明度
		nudge_x = xlimits - dt$log2FC, #标签x轴起始位置调整
		direction = "y", #按y轴调整标签位置方向，若想水平对齐则为x
		hjust = 0,
		fontface = "italic"
		) +
		labs(
		x = expression(log[2]("Fold Change")),
		y = expression(-log[10](adj.p-Value))
		y = expression(-log[10]("adj.p.Value"))
		) +
		guides(color = "none") +
		theme(plot.margin = unit(rep(1,4),'lines'))
		theme(
		plot.margin = unit(rep(1,4),'lines'),
		legend.position = legend_position,
		legend.title = element_blank(),
		text = element_text(family = font)
		)

		if(isTRUE(show_p))
		{
		plot <- plot +
		annotate(
		geom = "text",
		x = min(dt$log2FC),
		x = xlimits * -1,
		y = -log10(p_value),
		hjust = 0,
		vjust = 1,
		label = paste0("p-value = ",p_value)
		label = paste0("adj.p.Value < ",p_value),
		family = font
		)
		}

		@@ -367,10 +420,11 @@ volcano_plot <- function(
		plot <- plot +
		annotate(
		geom = "text",
		x = min(dt$log2FC),
		x = xlimits * -1,
		y = -log10(p_value) - 0.3,
		hjust = 0,
		label = paste0("Fold Change = ",fold_change)
		label = paste0("Fold Change > ",fold_change),
		family = font
		)
		}

		@@ -379,15 +433,17 @@ volcano_plot <- function(
		plot <- plot +
		annotate(
		"text",
		x = c(-log2(fold_change),min(dt$log2FC)) \|> mean(),
		y = max(dt$log10P),
		label = stat[regulation == "down",label]
		x = xlimits/2,
		y = max(dt$log10P) + 0.5,
		label = stat[regulation == "down",label],
		family = font
		) +
		annotate(
		"text",
		x = c(log2(fold_change),max(dt$log2FC)) \|> mean(),
		y = max(dt$log10P),
		label = stat[regulation == "up",label]
		x = xlimits/2 * -1,
		y = max(dt$log10P) + 0.5,
		label = stat[regulation == "up",label],
		family = font
		)
		}

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