Question: Plot local ancestry on chromosome
0
gravatar for Bioinformatics_NewComer
9 months 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 • 411 views
ADD COMMENTlink modified 7 months ago by bernatgel2.0k • written 9 months ago by Bioinformatics_NewComer320

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 It looks like Martin's approach is outdated.

ADD REPLYlink written 7 months ago by moxu440
1
gravatar for bernatgel
7 months ago by
bernatgel2.0k
Barcelona, Spain
bernatgel2.0k 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 7 months ago by bernatgel2.0k

Thank you. I'll look into it.

ADD REPLYlink written 7 months ago by Bioinformatics_NewComer320
1

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

ADD REPLYlink written 5 weeks ago by soulsacross60
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