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szpiech / selscan

Haplotype based scans for selection
GNU General Public License v3.0
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Plot iHs from selscan #19

Closed plxsas closed 8 years ago

plxsas commented 8 years ago

Dear Zachary A Szpiech,

Can you please help me with this matter?

I did manage to run the test of signature of selection using selscan and now I am trying to make a plot.

I am trying to use the r script you provide in src folder. Is this how it should be run, please?

plotHaplotypes(example.ihs.out) of course after running the function first.

I am looking forward to hearing from you.

Thanks

szpiech commented 8 years ago

The R script that I have posted (and which is completely undocumented, I admit) will plot haplotype structure surrounding a particular locus. It was something I wrote to play around with output from using the --ehh flag (it will use those inscrutable and undocumented *.colormap files) and isn't meant to be used with iHS output. If you wish to plot iHS scores you should just load the output file into R (i.e. data<-read.table("example.ihs.out")), and plot as usual.

If you want to check out what the plotHaplotypes() does, first source the script ("run the function") and then try plotHaplotypes("example.ehh.Locus4077.out") with the example data provided.