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Phylogenetic tree in Adegenet

I am using a R package called adegenet to plot the nj tree from plink files. In my plink file (input.raw) FID and IID are the same. So i have 3 questions here 1)Should FID be replaced with population name in the raw file? 2)Is there a way of providing population name separately in adegenet? 3)How can I color the clusters in a tree with different colours?

I did this

tre<-nj(D)
plot(tre, type = "unr", show.tip.lab = TRUE, cex=0.3, font=1, edge.col="Blue")

So all the edges turn blue. But i want edge color according to clusters. Is there a way?Ill appreciate any help.TIA!

adegenet phylogenetic tree plink
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written by akang akang

This is one way of doing it

  plot(tre, type = "unr", show.tip.lab = TRUE, cex=0.3, font=1, edge.col=c("Blue", "Red", "Green", "Yellow")[D$pop])
• 1 views • link
written by akang akang

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