SNP correlation to PCA eigenvectors

Question

[reid.j.thompson]

I am fairly new to PCA analysis and I am trying to understand a bit more. I have a collection of SNP genotypes (in VCF format) for 200 samples, and I am running PCA via SNPRelate (http://corearray.sourceforge.net/tutorials/SNPRelate/#principal-component-analysis-pca).

I am trying to better understand what the graph on "correlation to PC eigenvectors" means though (the colored plot under "To calculate the SNP correlations between eigenvactors and SNP genotypes:").

Does anyone have any idea how I should interpret this plot? Is it better to be uniformly distributed toward high numbers (1.0), or low numbers (0.0)? Again, I'm just not sure what this means.

Many thanks in advance!

Answer 1

[dago]

This was quite a good post:

How do I explain to my non-bioinformatician labmates how to interpret principal components?