karyoploteR: custom genome axis $latest.plot
0
0
Entering edit mode
Radek ▴ 90
@radek-8889
Last seen 5.9 years ago
Belgium

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 in-build genomes (hg19) but not for a custom genome.

Is this currently possible? Does someone has any idea how to do it? 

Thanks! 

 

KaryoploteR • 1.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 387 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6