Help making ADMIXTURE output digestible
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5.7 years ago
devenvyas ▴ 680

I am new to the program ADMIXTURE.

I am running it from K=1 to K=20 on a set of 2033 individuals and 276,899 SNPs post-LD-pruning. The sample order is based on the default order in the dataset I downloaded, so population members are not necessarily back-to-back and related populations are not necessarily listed near each other.

Ideally, in the morning I will have a set of 40 *.Q files (20 with CV and bootstrap and 20 without), so in preparation I am trying to figure out how to graph them with the bars in a meaningful order. I was wondering if anyone had suggestions on how to this (or general suggestions about managing ADMIXTURE output).

Thanks!

 

 

 

admixture • 3.8k views
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I have the exact same question! Here is a similar one: Can't figure out order of output rows in ADMIXTURE

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4.3 years ago
beausoleilmo ▴ 370

I found this website explaining how to do the full analysis. Basically, you have to look in the .fam file. You can import this file in R like this: fam = read.table("~/path-to-the-file/my_analysis.fam"). After that I was reusing the first column and rename the rows of your .Q file: tbl = read.table("~/path-to-the-file/my_analysis.Q"). Use this dataset to print your barplot!

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