#!/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 volcano 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.volcano_plots.pdf")

for (DE_file in DE_result_files_vec) {

    message("plotting volcano for: ", DE_file)
    data = read.table(DE_file, header=T, row.names=1)
    plot_Volcano(rownames(data), data$logFC, data$FDR, title=DE_file, top_gene_labels_show=args$top_genes_label)

}

dev.off()