How to get labels to not overlap other chromosomes?

[yonniejon]

What settings do I use to change the height between chromosomes?

[bernatgel]

Hi @yonniejon

What you need here is to change the "Plot Params". The idea is to create a plot.params object, modify the values you need and then use it as a parameter for plotKaryotype

Example:

pp <- getDefaultPlotParams(plot.type=2)
pp$leftmargin <- 0.3
pp$data2height <- 30
kp <- plotKaryotype(chromosomes=c("chr1", "chr2"), plot.type=2, plot.params = pp)

You can find more information at the karyoploteR tutorial: https://bernatgel.github.io/karyoploter_tutorial/Tutorial/PlotParams/PlotParams.html

These are the available parameters (you can create this image for your exact situation with plotDefaultPlotParams(plot.type=1)) but the parameter you need to increase is data1outmargin which I would set to something like 200 or so in your plot. Another thing that could help is to rotate the labels so they occupy less space. Try adding srt=45 to your call to kpPlotMarkers to see if this helps

[yonniejon]

Thank you!!! very helpful