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I am trying to plot ADMIXTURE output in R. My output is two-dimentional (two columns, 190 rows). These rows represent individuals, and groups of them (e.g., 1-12) represent populations. I have eleven populations. What I'm hoping for is a plot with eleven different colours, basically like a STRUCTURE plot.

This code works, but plots with only two colours, not separating the populations

>tbl=read.table("filepath to file",sep=" ")
#plotting
> barplot(t(as.matrix(tbl)), col=rainbow(4),
xlab="Individual #", ylab="Ancestry", border=NA)

I have tried to amend this with the following code:

>barplot(t(as.matrix(tbl[c(0:12, 13:32, 33:51, 52:69, 70:87, 88:104, 105:118, 119:137, 138:157, 158:172, 173:190), ])), 
col=c("darkgreen", "darkblue", "orange", "cyan", "yellow", "chartreuse", "blue", "cyan4", "red", "violet", "blueviolet"), 
xlab="Individual #", ylab="Ancestry", border=NA)

but this code really still says the same thing c(1:190)

Alternatively, this code separates the colours

barplot(t(as.matrix(tbl))[1],
    col=c("darkgreen", "darkblue", "orange", "cyan", "yellow", "chartreuse", "blue", "cyan4", "red", "violet", "blueviolet")
    [c(rep(1,length(1:12)),rep(2,length(13:32)), rep(3,length(33:51)), rep(4,length(52:69)), rep(5,length(70:87)), rep(6,length(88:104)), 
    rep(7,length(105:118)), rep(8,length(119:137)), rep(9,length(138:157)), rep(10,length(158:172)), rep(11,length(173:190)))],
    xlab="Individual #", ylab="Ancestry", border=NA)

But this only plots in one dimension. I've tried so many permutations of the concepts in each of these, and I just can't get it.

I've tried available code on the net, but I think my R skills aren't advanced enough to sort out their tricks. Any suggestions would be much appreciated.

Sincerely, Ella

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This question is off-topic as it is not about biology, but about using R. While we allow questions about tools used by biologists, this question is entirely about programming/graphing and not on-topic here. –  Mad Scientist Nov 8 '13 at 6:59
1  
@Ella Just to clarify - you should ask this question at stackoverflow.com where it is clearly on-topic. –  fileunderwater Nov 8 '13 at 9:28
    
Ok, thanks for this. I've actually sorted out my problem now anyway, so I think I will not pursue it further. –  Ella Nov 12 '13 at 20:16
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closed as off-topic by Mad Scientist Nov 8 '13 at 6:59

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