SNPRelate: how to give specific color to a population in PCA plot

Question

[kumar.vinod81]

I am using SNPRelate for PCA analysis. Its using default color for different populations but I want to color them according to me. Plotting commands are like this:

> plot(tab$EV2, tab$EV1, col=as.integer(tab$pop),cex=1.2,pch=20,
+ xlab="eigenvector 2", ylab="eigenvector 1")
> legend("topleft", legend=levels(tab$pop), cex=1,pch=20, col=1:nlevels(tab$pop))

Head of the input file is like this:

sample.id   pop         EV1         EV2
1        A1 POP_I -0.10172849  0.03619405
2        A2 POP_I -0.15951814  0.08234857
3        A3 POP_I -0.15632495  0.08180843
4        A4 POP_I -0.09679447  0.07981108
5        A5 POP_I  0.11362360 -0.03186038
6        A6 POP_I  0.05594095 -0.05498351

Any idea about it?

Answer 1

[coleman_jonathan]

I think you want to use R's palette command.

[waqaskhokhar999]

How we can label the samples in this PCA plot?