Hi! I want to create manhattan plots for genome-wide association studies (-log(p) ~ SNPs). I wonder whether there is a recommended approach avoiding the problems I have with the functions named below Im my data I have only significant SNPs for dozens of similar phenotypes using different association models. This means some chromosomes are not represented and some SNPs multiple times in my data, which could cause some confusion in the plotting functions below. This is what my data looks like: chrom pos p trait model SNP1 1 10 1E-05 qt1 simple SNP2 1 20 1E-10 qt2 simple SNP2 1 20 1E-11 qt3 adjusted SNP3 1 40 1E-02 qt4 simple ... Solutions so far: The simple *plot ()* function prints error bars in my data as some SNPs are represented multiple times (due to multiple phenotypes/models). *sunflowerplot()* works rather well. Both functions label the x-axis with snp names which are not readable if a great number of SNPs examined at once. I have found the *mhtplot ()* function in the <gap> package. However, it gives error messages and just plots fragments of the plot. I found the *wgplot ()* function (http://bioinfo-mite.crb.wsu.edu/Rcode/wgplot.R) which tries to fix some bugs in mhtplot(). This works rather well, but it sometimes screws up with the x-axis labels which are printed on the x-axis or are sometimes missing. Any suggestions? Thanks in advance, Will