Question: Generating an ADMIXTURE plot that stacks the different values of K using R
0
gravatar for devenvyas
3.5 years ago by
devenvyas580
Stony Brook
devenvyas580 wrote:

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.

admixture R • 2.4k views
ADD COMMENTlink modified 11 months ago by RamRS23k • written 3.5 years ago by devenvyas580

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

ADD REPLYlink modified 11 months ago by RamRS23k • written 3.5 years ago by Mo890

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

ADD REPLYlink modified 11 months ago by RamRS23k • written 3.5 years ago by devenvyas580
0
gravatar for ivivek_ngs
3.5 years ago by
ivivek_ngs4.8k
Seattle,WA, USA
ivivek_ngs4.8k wrote:

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

ADD COMMENTlink modified 11 months ago by RamRS23k • written 3.5 years ago by ivivek_ngs4.8k

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.

ADD REPLYlink modified 11 months ago by RamRS23k • written 3.5 years ago by devenvyas580

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

ADD REPLYlink written 3.2 years ago by hellbio370

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

ADD REPLYlink written 3.1 years ago by devenvyas580
0
gravatar for Marco.Milanesi
14 months ago by
Marco.Milanesi0 wrote:

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)

ADD COMMENTlink modified 11 months ago by RamRS23k • written 14 months ago by Marco.Milanesi0
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