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!