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#!/usr/bin/env Rscript
suppressPackageStartupMessages(library("argparse"))
initial.options <- commandArgs(trailingOnly = FALSE)
file.arg.name <- "--file="
script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
script.dirname <- dirname(script.name)
source(paste0(script.dirname,"/R/rnaseq_plot_funcs.R"))
parser = ArgumentParser(description="generate MA plots in DE directory")
parser$add_argument("--top_genes_label", help="number of top DE genes to label in the plot", type="integer", default=20)
args = parser$parse_args()
DE_result_files_vec = dir(pattern='DE_results$')
pdf("DE_results.MA_plots.pdf")
for (DE_file in DE_result_files_vec) {
message("plotting MA plot for: ", DE_file)
data = read.table(DE_file, header=T, row.names=1)
plot_MA(rownames(data), data$logCPM, data$logFC, data$FDR, title=DE_file, top_gene_labels_show=args$top_genes_label)
}
dev.off()
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