When combining multiple GWAS results into a stacked manhattan plot using KaryoploteR, how do you label top SNPs in each set of GWAS results? Instructions provided for labelling a single manhattan plot did not work for the stacked manhattan.
You should be able to apply the snp labelling code to the stacked manhattan using almost the same code provided in the example. The key is to give the same autotrack you use for kpPlotManhattan to the functions used for labeling (kpPoints and kpText, for example).
Does it make sense? You should replicate the labeling code as you replicate the call to kpPlotManhattan and give all functions plotting in the same "track" the same autotrack configuration.
If this is not clear yet, I can provide a small example. Just ask.