Plot local ancestry on chromosome

Question

[Bioinformatics_NewComer]

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

[moxu]

Any luck? It looks like Martin's approach is outdated.

[devenvyas]

Did you ever find a solution? The Martin approach hard limits to three reference populations.

Answer 1

[bernatgel]

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...)

[Bioinformatics_NewComer]

Thank you. I'll look into it.

[cruzpedro]

Hi, I have just posted an example karyoploteR code in another post