Question: karyoploteR: custom genome axis $latest.plot
0
gravatar for VHahaut
5 months ago by
VHahaut1.0k
Belgium
VHahaut1.0k 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 • 280 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 5 months ago by VHahaut1.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1426 users visited in the last hour