#!/usr/bin/env Rscript library(ggplot2) args = commandArgs(trailingOnly=TRUE) tab <- read.table(args[1], header=T, sep="\t") colnames(tab) <- c("dijarn", "gene") tab$dijarn <- factor(tab$dijarn, levels = tab$dijarn[order(tab$gene)]) p <- ggplot(tab, aes(x= dijarn, y = gene)) p <- p + geom_point(shape = 20, color = "red", size = 3) p <- p + theme_classic() pdf_name <- paste(args[4],"/", args[2],"/plots/genes_by_TADs_",args[2], "_", args[3],".pdf", sep="") print(pdf_name) pdf(pdf_name) p dev.off()