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Examining Principal Components of Genetic Ancestry in R

Hi All,

I want to examine the population structure using genotyped data. Using the smartpca program from the eigensoft package, I calculated principal components of genetic data using 'smartpca -p mydata > pca.log' command. Finally, I have got a lot of stuff in the file name 'pca.log' including removal of outliers (5 iteration), Tracy-Widom statistics, top 10 eigvalues, 10 eigenvector..etc.

Now, i don't have any idea how to plot the population structure in R software package. Does anyone have R script to plot using the first two principal components of genetic ancestry?

Thank you for your time!

pca r
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updated by anp375 anp375 • written by tesfadej2003 • tesfadej2003

2 answers

I think this page has what you're looking for.

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written by Jean-Karim Heriche Jean-Karim Heriche

First of all, thank you very much for your helpful hint. I have seen it the link and tried to adopt it. However, it is not working. I understood all the outputs from 'smartpca -p Itamba.par > Itamba.out' should be in the file 'Itamba.out'. So, 'Itamba_PCA.evec' and 'Itamba_PCA.eval' were not created as separate output file and I couldn't find inside 'Itamba.out' output file. Is there a way to create these two output files from the main output file ('Itamba.out')? Becuase it has been used separately.

Thank you in advance.

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written by tesfadej2003 • tesfadej2003

Not all the output is in one file. The output file names are specified in a configuration file. In this example, the configuration file is called Itamba.par and in this file, the file 'Itamba_PCA.evec' (containing the PCs/eigenvectors) should be specified as value for the parameter named 'evecoutname' i.e. as
'evecoutname:'Itamba_PCA.evec'. Same for eigenvalues and parameter 'evaloutname'. These parameters should be required so check that you have specified the correct file name/path and/or that you don't get any error message.

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written by Jean-Karim Heriche Jean-Karim Heriche

Samples Eigenvector1 Eigenvector2 Eigenvector3 ... EigenvectorX

Sample1 Xcoord_____Ycoord_____Zcoord

Sample2 Xcoord_____Ycoord_____Zcoord

. . .

SampleN Xcoord_____Ycoord_____Zcoord

Plot 1 point for each sample using two of the three coordinates. Or plot all three at the same time using this package: https://cran.r-project.org/web/packages/pca3d/pca3d.pdf

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written by anp375 anp375

Thank you. You gave me hint to plot 3D. What I need is to plot 2D?

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written by tesfadej2003 • tesfadej2003

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