R plot.DNAcopy with x-axis showing chromosome instead of chromosome coordinate

Question

[CY]

I was trying to plot CNV with plot.DNAcopy (a function in DNAcopy library). The input is standard DNAcopy segment file.

Can anyone share some guidance on how to change x-axis from chromosome coordinate to chromosome? Thanks

[goodez]

Try saving the plot.DNAcopy as an object. You could then look for object$data or something similar (I'm not sure how plot.DNAcopy is structured) and save that as data to plot with your own custom plot, like ggplot2 or base functions.

I've done something similar in the past when I wanted more control of the plotting.