rgb to hex in GRanges Object in R
Hey,
I have the following problem: using the karyoploteR package in R, i want to plot chromatin configuration along the genome as a colored bar. The GRanges Object with the chromatin regions has a column for that ("V9") with rgb values associated with each region. However, the kpPlotRegions function requires the colors in hex-format. I tried to export the Object, change rgb to hex and re-import it, but doesn't recognize the input. Has anyone experienced this problem or could provide a solution? Thank you!
K562.hmm
GRanges object with 622257 ranges and 6 metadata columns:
seqnames ranges strand | V4 V5
<Rle> <IRanges> <Rle> | <character> <integer>
1 chr1 10000-10600 * | 15_Repetitive/CNV 0
2 chr1 10600-10937 * | 13_Heterochrom/lo 0
3 chr1 10937-11937 * | 8_Insulator 0
4 chr1 11937-12337 * | 5_Strong_Enhancer 0
5 chr1 12337-13137 * | 7_Weak_Enhancer 0
... ... ... ... . ... ...
622253 chrX 155256806-155257806 * | 11_Weak_Txn 0
622254 chrX 155257806-155259206 * | 8_Insulator 0
622255 chrX 155259206-155259406 * | 6_Weak_Enhancer 0
622256 chrX 155259406-155259606 * | 7_Weak_Enhancer 0
622257 chrX 155259606-155260406 * | 15_Repetitive/CNV 0
V6 V7 V8 V9
<character> <integer> <integer> <character>
1 . 10000 10600 245,245,245
2 . 10600 10937 245,245,245
3 . 10937 11937 10,190,254
4 . 11937 12337 250,202,0
5 . 12337 13137 255,252,4
... ... ... ... ...
622253 . 155256806 155257806 153,255,102
622254 . 155257806 155259206 10,190,254
622255 . 155259206 155259406 255,252,4
622256 . 155259406 155259606 255,252,4
622257 . 155259606 155260406 245,245,245
-------
seqinfo: 23 sequences from an unspecified genome; no seqlengths
> kpPlotRegions(kp, K562.hmm, col=K562.hmm$V9, r0=0.22, r1=0.3)
Error in (function (xleft, ybottom, xright, ytop, density = NULL, angle = 45, :
Unzulässige Farbspezifikation "245,245,245"
1 answer
The rgb conversion shown here should help. I.e.
sapply(strsplit(K562.hmm$V9, ","), function(x)
rgb(x[1], x[2], x[3], maxColorValue=255))
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Friederike
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Can you show the error you get with the hex-format?
Thank you for your answer! There is no distinct error: When i import a file with hex-values, it just doesn't recognizes them and prints NA only.
probably due to the
#, you would have to tweak the import settings of the function you're using. But see if the function I linked below already does what you want directly on the RGB values.