Commit ed42f984 authored by Beatrice Tan's avatar Beatrice Tan
Browse files

Attempt to plot regions.

parent 914ac322
...@@ -60,4 +60,4 @@ rule compare_regions: ...@@ -60,4 +60,4 @@ rule compare_regions:
output: output:
plots=expand("Reports/Overlap_plots/{region}.png", region=get_regions(input.overlap)) plots=expand("Reports/Overlap_plots/{region}.png", region=get_regions(input.overlap))
shell: shell:
"R {workflow.basedir}/scripts/karyoploteR" "R {workflow.basedir}/scripts/plot_regions.R"
#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
source("https://bioconductor.org/biocLite.R")
biocLite("karyoploteR")
bed = read.table(args[1], sep="\t", header=TRUE)
#Read output plot files?
#chrom as "chr1"
kp <- plotKaryotype(chromosomes=c(chrom))
#kpDataBackground(kp)
kpAxis(kp)
kpRect(kp, chr=chrom, x0=start, x1=end, y0=0.2, y1=0.4)
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