Attempt to plot regions.

rules/ComparisonRegions.smk

@@ -60,4 +60,4 @@ rule compare_regions:
     output:
         plots=expand("Reports/Overlap_plots/{region}.png", region=get_regions(input.overlap))
     shell:
-        "R {workflow.basedir}/scripts/karyoploteR"
+        "R {workflow.basedir}/scripts/plot_regions.R"

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)