Biostars beta testing.
Question: Plot local ancestry on chromosome
0
Entering edit mode

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

ADD COMMENTlink 16 months ago Bioinformatics_NewComer • 320 • updated 14 months ago bernatgel ♦ 1.9k
Entering edit mode
0

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 It looks like Martin's approach is outdated.

ADD REPLYlink 14 months ago
moxu
• 440
1
Entering edit mode

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...)

ADD COMMENTlink 14 months ago bernatgel ♦ 1.9k
Entering edit mode
0

Thank you. I'll look into it.

ADD REPLYlink 14 months ago
Bioinformatics_NewComer
• 320

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.0