How to plot PCA figure using Genesis software?

Question

[sayyarsehrish]

I have generated PCA files using plink (eigenvec and eigenval). now I am trying to plot PCA figure using genesis software. but the figure doesn’t give me any information about group showing no group. how can I sort out this error. genesis need phenotype file and have no phenotype file.

[zx8754]

On Page 16 of Genesis manual, they describe the expected input. It is a reformatted version of output from SNPRelate R package.

How does your input data looks like? Try to reformat it to match with the manual and test.

[4galaxy77]

If you have the data already in the plink output format, it's easy to plot in R. If you have a column for population, you could do something like:

eigenvectors %>%
    ggplot(aes(x=PC1, y=PC2, colour=pop)) +
    geom_point()

Which avoids the need to convert to a different format.

[sayyarsehrish]

i have data in plink output format but i have no information about different groups in data output.

[4galaxy77]

You need to add those yourself.