Question: karyoploteR: custom genome axis $latest.plot
0
gravatar for VHahaut
17 months ago by
VHahaut1.1k
Belgium
VHahaut1.1k wrote:

Hi!

I would like to dynamically modify the axis from custom genomes plotted with karyoploteR.

Example:

library(karyoploteR)
custom.genome <- toGRanges(data.frame(chr="chr1", start=1, end=10e7)
kp <- plotKaryotype(genome = custom.genome)
regions <- GRanges(seqnames=rep("chr1", 100), IRanges(start=round(runif(100,min = 100, max=10e7)), width=10000))
kpPlotDensity(kp, data=regions)

Then use:

kpAxis(kp, ymax=kp$latest.plot$computed.values$max.density, r0=0, r1=1, cex=0.8)

In order to get an ymax properly representing my data. So far it seems to work for hg19 but not for a custom genome. Does someone knows how to deal with this?

Thanks!

karyoploter R • 643 views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 17 months ago by VHahaut1.1k
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