Simple ideogram plotting and annotation in R.
Basic usage:
Rscript Ideoplot.R --heatmap hm.bed --annotate annotations.bed --out ideogram.pdf
-or-
Rscript Ideoplot.R --annotate annotations.bed
Options
--ideobed, i A bed file of reference contig lengths/chromosome names
--heatmap, -h Fill chromosomes with normalized heatmap
(described below)
--annotate, -a Add character annotations.
--out, -o PDF output name.
--stripes, -s Specify a file containing the layout of the
annotations (description below)
--bars, -b Add track annotations
--reference, -f Either hg19, or hg38
--topdown, r Flag, when set, flips the orientation (P arms
drawn on top).
