File: plot_comparison.Rscript

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#!/usr/bin/env Rscript

charlotte = read.table("tximport.counts.dat")
mine = read.table("salmon.gene.counts.matrix")

mine = mine[rownames(charlotte),] # ensure in same order

samples = colnames(mine)

pdf("compare.pdf")

for (sample in samples) {

	c_sample = paste0('c_', sample)
    plot(log2(mine[,sample]+1), log2(charlotte[,c_sample]+1), main=sample)
}