I've been trying to generate two Manhattan plots of different data sets to compare. However, one problem I'm facing with e.g. qqman and other R plotting scripts I've tried is that the plots don't align when e.g. overlaid (which is quite visible, as the boundaries of the single chromosomes are shifted). I assume this is because e.g. in data set 1, chromosome 1 contains data points from a certain positional range, whereas this range might be smaller or larger in the second data set. I've not been able to find a script that would allow me to set this range.
Is anyone aware of any Manhattan plotting software, scripts or packages that would be able to do this?