Thank you. I'll look into it.
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Plot local ancestry on chromosome
I've per chromosome, per SNP composition from three ancestries using ELIA for each individual. I'd like to plot these information. Is there any R package that can help?
Output as:
0.107 0.995 0.898
0.992 0.001 1.007
0.597 1.402 0.001
1.998 0.001 0.001
0.933 0.011 1.056
1.023 0.965 0.013
1.999 0.001 0.000
1.831 0.017 0.152
0.900 0.002 1.099
1.947 0.000 0.053
SNP composition for first ten individuals for one SNP.
I found pipeline using RfMix's output https://github.com/armartin/ancestry_pipeline
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bernatgel
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Bioinformatics_NewComer
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1 answer
Hi,
To create an image similar to the one in the link, you can use karyoploteR. You'll need the position of each of the SNPs, in addition to your values.
There is a complete tutorial on creating plots at the karyoploteR tutorial page. You'll have to decide exactly what do you want to use to represent your data (rectangles, points, etc...)
Hi, I have just posted an example karyoploteR code in another post
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Any luck? It looks like Martin's approach is outdated.
Did you ever find a solution? The Martin approach hard limits to three reference populations.