Question: Plot local ancestry on chromosome
0
gravatar for Bioinformatics_NewComer
2.0 years ago by
Genomic Island
Bioinformatics_NewComer320 wrote:

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

plot ancestry • 1.1k views
ADD COMMENTlink modified 23 months ago by bernatgel2.7k • written 2.0 years ago by Bioinformatics_NewComer320

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 It looks like Martin's approach is outdated.

ADD REPLYlink written 23 months ago by moxu460

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

ADD REPLYlink written 7 months ago by devenvyas650
1
gravatar for bernatgel
23 months ago by
bernatgel2.7k
Barcelona, Spain
bernatgel2.7k wrote:

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 written 23 months ago by bernatgel2.7k

Thank you. I'll look into it.

ADD REPLYlink written 23 months ago by Bioinformatics_NewComer320
1

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

ADD REPLYlink written 16 months ago by cruzpedro60
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