Plot for PCA
I tried to do pca in plink. I got .eigenvec and .eigenval files. I want to draw a plot. In .eigenvec file, I have family ID column, sample individual ID column and 20 PC columns,respectively. Should I use first two PC columns? How can I draw a plot? I tried to draw in R using first two PCs and got a plot but I need to colour up it and give population names. How can I figure it out?
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GenoMax
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genogeno •
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PCA has been well described and tons upon tons of help are available. Your question alone has been answered hundreds of times. Try Factominer package in R since it's seems you are not building the plot from scratch.