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Generating an ADMIXTURE plot that stacks the different values of K using R

I am trying to create an ADMIXTURE figure a publication where I display my results for different values of K vertically on top of each other. I am looking for something like Figure S1 from this paper.

I was wondering if anyone here know how to do this?

The only other alternative I know is to use Illustrator, but I am thinking there must be some R-based method of doing this.

r admixture
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updated by Ram Ram • written by devenvyas devenvyas

@devenvyas Please give an example data and explain what you have tried (if possible)

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updated by Ram Ram • written by Mo Mo

For every value of K, I have a table that looks like this (so I have 19 tables with a different number of columns)

iid         Q0  Q1  Q2  Q8  pop region  bigregion   verbosepop  number
sample1     #   #   #   #   pop1    r1  big1        pop1        1
sample2     #   #   #   #   pop1    r1  big1        pop1        2
sample3     #   #   #   #   pop1    r1  big1        pop1        3
sample4     #   #   #   #   pop1    r1  big1        pop1        4
sample5     #   #   #   #   pop2    r2  big2        pop2a       5
sample6     #   #   #   #   pop2    r2  big2        pop2a       6
sample7     #   #   #   #   pop2    r2  big2        pop2a       7
sample8     #   #   #   #   pop2    r2  big2        pop2b       8
sample9     #   #   #   #   pop2    r2  big2        pop2b       9
sample10    #   #   #   #   pop3    r2  big2        pop3a       10
sample11    #   #   #   #   pop3    r2  big2        pop3b       11

I have not tried anything, because I have no idea where to start. I have scripts that will generate population means for each pop and then graph out the result for one value of K, so I have 19 pdf files that I can stitch together using Illustrator, but I would prefer to get R to do it. I am trying to find a script that can graph all of them into a format similar to Figure S1 from this paper

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updated by Ram Ram • written by devenvyas devenvyas

2 answers

You can try to use a new R packege called BITE.
The function membercoef.circos plots a similar result in a circular way, as reported in the README file)

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updated by Ram Ram • written by Marco.Milanesi • Marco.Milanesi

May be this biostar post might be of some help. Have a look.

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updated by Ram Ram • written by ivivek_ngs ivivek_ngs

That's not what I am looking for (or at least the way it is described it isn't)

I know how to plot ADMIXTURE results for individual values of K, I am trying to find a way to get R to plot results for different numbers of K. I am looking for something like Figure S1 from this paper.

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updated by Ram Ram • written by devenvyas devenvyas

Hi, i am in a similar need. Have you figured out how to generate the plot shown in S1 in the article?

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written by hellbio hellbio

Nope, I ended up just generating the plots individually and then stacked them in Adobe Illustrator.

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written by devenvyas devenvyas

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