modified RNA-seq.R in R (cbdedb6c) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+24 −15

Original line number	Diff line number	Diff line
		@@ -162,6 +162,7 @@ de.gene <- function(
		}
		}


		volcano_plot <- function(
		.data,
		top_gene_number = 10,
		@@ -171,6 +172,7 @@ volcano_plot <- function(
		show_p = TRUE,
		show_fc = TRUE,
		show_gene_number = TRUE,
		show_legend = FALSE,
		sub_gene = NULL,
		sub_id = NULL,
		color_up = "#E64B35",
		@@ -256,31 +258,33 @@ volcano_plot <- function(
		aes(log2FC,log10P),
		color = color_ns,
		size = 0.8,
		show.legend = F
		show.legend = show_legend
		) +
		geom_point(
		data = dt[color == "up"],
		aes(log2FC,log10P),
		color = color_up,
		size = 0.8,
		show.legend = F
		show.legend = show_legend
		) +
		geom_point(
		data = dt[color == "down"],
		aes(log2FC,log10P),
		color = color_down,
		size = 0.8,
		show.legend = F
		show.legend = show_legend
		) +
		geom_point(
		data = dt[color == "special"],
		aes(log2FC,log10P),
		color = color_special,
		size = 0.8,
		show.legend = F
		show.legend = show_legend
		)

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

		plot <- plot +
		geom_hline(
		yintercept = -log10(p_value),
		@@ -291,21 +295,26 @@ volcano_plot <- function(
		xintercept = c(-log2(fold_change),log2(fold_change)),
		linetype = fc_line_type,
		color = right_fc_line_color
		)
		) +
		xlim(xlimits * -1, xlimits)
		}else{
		if(abs(min(dt$log2FC)) <= abs(max(dt$log2FC))){
		hyperbola_dt_r <- dt[log2FC > 0,.(log2FC,hyperbola_log10P)]
		hyperbola_dt_l <- dt[log2FC > 0,.(log2FC = log2FC * -1, hyperbola_log10P)]
		}else{
		hyperbola_dt_r <- dt[log2FC < 0,.(log2FC,hyperbola_log10P)]
		hyperbola_dt_l <- dt[log2FC < 0,.(log2FC = log2FC * -1, hyperbola_log10P)]
		}

		hyperbola_dt <- rbind(hyperbola_dt_l,hyperbola_dt_r)

		plot <- plot +
		geom_line(
		data = dt[log2FC < 0],
		data = hyperbola_dt,
		aes(log2FC,hyperbola_log10P),
		linetype = fc_line_type,
		color = left_fc_line_color
		) +
		geom_line(
		data = dt[log2FC > 0],
		aes(log2FC,hyperbola_log10P),
		linetype = fc_line_type,
		color = right_fc_line_color
		) +
		scale_y_continuous(limits = c(0,max(dt$log10P) + 1))
		}

		@@ -362,10 +371,10 @@ volcano_plot <- function(
		plot <- plot +
		annotate(
		geom = "text",
		x = log2(fold_change) + 0.1,
		y = max(dt$log10P) + 1,
		x = min(dt$log2FC),
		y = -log10(p_value) - 0.3,
		hjust = 0,
		label = paste0("Fold Change threshold = ",fold_change)
		label = paste0("Fold Change = ",fold_change)
		)
		}

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