How do I perform a plot from admixture analysis with multiple runs
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Entering edit mode
6 days ago

Hi all,

I am wondering how I can perform a plot from admixture analysis with multiple runs. I have obtained 100 runs for each K value from 1 to 10. So my question is what to do with the multiple .P and .Q files obtained from this analysis to make the plot.

Any suggestion?

multiple admixture plot runs • 159 views
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Entering edit mode
4 days ago

I found the answer, you need first to move all *Q files from each K into a single folder. Next, you should process this folder using 'pophelper' in R, using the following command:

remotes::install_github('royfrancis/pophelper')

library('pophelper')

setwd('/Users/alexisdiaz/Desktop/popgen/admixture_analysis/admixture_macosx/results2')

afiles <- list.files(path=".", full.names=T)

alist <- readQ(files=afiles)

readQ(files=afiles, filetype = 'basic')

clumppExport(alist, exportpath=".")

Pophelper will create 'paramfiles' and combined txt files in folders per each K. Next, make sure you place clumpp.exe file into each folder, click on the executable file and it will generate three other files. Use the *-combined-merged, copy values and plot it in excel.

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