karyoploteR: custom genome axis $latest.plot
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Radek ▴ 80
@radek-8889
Last seen 2.8 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 • 425 views
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