Manhattan Plots in R for Gene Expression

[P-Richmond]

I'm trying to visualize gene expression on a genome-wide basis, and I'd like to accomplish this via a Manhattan Plot (part of the R 'gap' package). Does anyone have experience with this? The manual on how to do this doesn't go into any detail on file format input or data organization.

If there is some other way to visualize gene expression on a genome wide basis (divided up by chromosomes) then please point me in the right direction.

Thanks,
Phil