Hello,
the title is pretty much the whole question.
I have identified potential selective sweep regions and I want to plot the allele frequencies of each site in this region using a stacked barplot (or something that looks like one). The regions contain 20-30 thousand sites, so I need to plot many bars. I tried R's standard barplot function and ggplot2 but there are so many bars that everything is just black.
I wonder if anyone knows a way to make such a plot. Best would be a R solution, but I'm also open for another software or python (although I just started to learn python, so R would be better).
Thank in advance.
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written
by
thal •
1 answer
1) You could do something similar to a manhattan plot, used for GWAS data. On the X you plot the position, on the Y you plot the allele frequency 2) You could work in windows, and plot the average MAF in a window of X Kb ofr Y SNPs.
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Perhaps look at a beeswarm plot.
Another option is to make your data in a form that can be rendered as a "stacked" or overlay view of Wiggle data in a UCSC Genome Browser, where scores are frequencies. This blog post goes into more detail about this view type: http://blog.openhelix.eu/?p=19029