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
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