I am trying to generate a manhattan plot from my genetic data for 5 traits (in separate txt files) in R. I want to gather them on one manhattan plot with different colours for different traits. I got stuck with the qqman package as the colours are assigned to the chromosomes not the traits. With the CMplot package it was working more than 12 hours and still got nothing. Can anyone suggest how can I imporove my thinking ;)
qqman package CMplot package