Good morning,
I'm doing a research on GWAS and I've obtained some file .eigenvec and .eigenval after executing the command --pca on PLINK 1.9.
How can I plot those files? What software can i use for this purpose?
Thank you in advance
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written
by
danielestrife •
This is straightforward in R.
Load the .eigenvec file. E.g. eigenvec_table <- read.table('plink.eigenvec')
Use plot() on the columns you're interested in. Top eigenvector will be in column 3, second eigenvector will be in column 4, etc., so if you want a set of pairwise plots covering the top 4 eigenvectors, use e.g. plot(eigenvec_table[3:6])
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written
by
chrchang523
Hi Chris, Why there is a "#" in the header of plink2.eigenvec? when R read "plink2.eigenvec", "#" line will be ignored
That depends on how you read the file with R.
For consistency with VCF, practically all plink2-output header lines start with ‘#’.
how to specify the colors to the different samples before plot pca?
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Relevant post: Gwas Stepwise Tutorial
Thank you that's what I need