Create Triangle Plot from Inferred Genetic Ancestry

I previously posted on how to infer ancestry for a group of study participants using SNP genotypes.  Today, I want to visually plot some of the output in R.  Two informative plots that can be generated from the output are a standard plot of the two eigenvectors with percent ancestry overlaid and a triangle (or ternary) plot with each axis representing percentage of one of the three ancestral populations (ex: European, African, and Asian).

Here is some simple code to plot this in R.  There is no base package to plot the triangle plot, so the plotrix package will need to first be installed.  The ancestry.txt file is the output file from SNPWEIGHTS, but other output could be formatted to work as well.

	# EV Plot with Percent Ancestry Overlay
	data=read.table("ancestry.txt", as.is=T, header=F)
	names(data) <- c("ID", "Case", "SNPs", "EV1", "EV2", "EUR", "AFR", "ASN")
	plot(data$EV1, data$EV2, pch=20, col="gray", xlab="EV1", ylab="EV2")
	text(data$EV1, data$EV2,labels=round(data$EUR,2)*100, cex=0.4, offset=0.1, pos=3)
	text(data$EV1, data$EV2,labels=round(data$AFR,2)*100, cex=0.4, offset=0.1, pos=2)
	text(data$EV1, data$EV2,labels=round(data$ASN,2)*100, cex=0.4, offset=0.1, pos=1)
	# Triangle Plot
	data$total=data$EUR+data$AFR+data$ASN # Need to account
	data$European=data$EUR/data$total # for slight rounding
	data$African=data$AFR/data$total # in the ancestry
	data$Asian=data$ASN/data$total # estimation file for
	data_p=data[c("European","Asian","African")] # triax.plot to work
	library(plotrix)
	triax.plot(data_p, pch=20, cc.axes=T, show.grid=T)

view raw plot_ancestry.R hosted with ❤ by GitHub

The output should look similar to the plots below.