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).
To swap to a different reference version, use the --ideobed option to specifiy an alternative ideogram bed file.
The ideogram bed file and coordinates are obtaned from ucsc: http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=364576305&clade=mammal&org=Human&db=hg19&hgta_group=map&hgta_track=cytoBandIdeo&hgta_table=0&hgta_regionType=genome&position=chrX%3A146991161-146996160&hgta_outputType=selectedFields
The layout geometry is organized in terms of stripes for each chromosome. The current layout is default at (5,5,15,10), where there are two stripes of width 5, one of width 15, and one of 10. The chromosome is drawn in the 3rd stripe (width 15). Annotations can go into any stripe. The widths of stripes are relative.
The stripes may be changed using the option -s stripes.txt, where the format of stripes.txt is stripe_width stripe_label, with the single reserved label "c" to label which stripe to draw the chromosome in. The default stripes are described in
5 a 5 a 5 a 15 c 10 s
Although here the 'a' and 's' don't mean anything, it is just not 'c'.
For now drawing of banding is disabled, but that will be done... soon.
There are three ways to annotate an ideogram: rectangles, annotations, and a heatmap.
Rectangles are bars drawn roughly the width of the stripes. chrom start end stripe color Example: ...
chr1 32665 63507 1 green chr1 163156 194165 1 green chr1 731738 740486 1 green
You can have Ideoplot try and have fancy coloring of enumerated groups by adding an additional column. Columns with group index 0 are rendered with the value in the color column. Group indices greater than 0 are assigned a color, hash combination so that each group has a unique color, hash. Right now up to 420 combinations are supported, but it's pretty hard to distinguish lots of them so that may change.
chrom start end stripe color index Example: ...
chr1 32665 63507 1 green 0 chr1 163156 194165 1 green 1 chr1 731738 740486 1 green 2 chr4 117223 497282 1 green 1
Finally you can add a strand to the plot with an additional column:
chrom start end stripe color index strand Example: ...
chr1 32665 63507 1 green 0 0 chr1 163156 194165 1 green 1 1 chr1 731738 740486 1 green 2 -1 chr4 117223 497282 1 green 1 1
-1: ignore strand 0: forward 1: reverse
The annotations are characters (for now just points, eventually text as well) that are drawn. Each column is:
chrom start end stripe pch color
Example: ...
chr1 39411519 39413487 2 23 "#377eb8" chr1 46169019 46171853 2 23 "#377eb8" chr1 46176404 46178211 2 23 "#377eb8" chr1 55705907 55707516 2 23 "#377eb8" chr1 73595641 73603844 1 15 "green" chr1 82721748 82724869 1 15 "green" chr1 87512436 87514550 1 20 "blue"
...
The stripe is the stripe to render the point. So, for a stripe layout of (5,5,15,10), the first 4 points are drawn in the 2nd stripe (position 5), and last 3 are drawn in the 1st stripe (pos 0).
The pch and the color are the colors to draw the annotation.
The heatmap is specified by a bed file with:
... chr1 20000000 25000000 4351 chr1 25000000 30000000 4574 chr1 30000000 35000000 9274 ...
The 4th column is some value that scales the heatmap. For now this is normalized by chromosome and scaled into 9 possible colors.