scripts/plot_infercnv_obj.R

In broadinstitute/infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data

#!/usr/bin/env Rscript

suppressPackageStartupMessages(library("argparse"))
    
parser = ArgumentParser()
parser$add_argument("--infercnv_obj", help="infercnv_obj file", required=TRUE, nargs=1)
args = parser$parse_args()

library(infercnv)

infercnv_obj_file = args$infercnv_obj

infercnv_obj = readRDS(infercnv_obj_file)

plot_cnv(infercnv_obj,
         output_filename=basename(infercnv_obj_file))