I used plotPCA function from DESeq2 to generate PCA (using the code plotPCA(rld)) for 2 groups of samples (untreated and treated). The sample dots look a bit far away from each other although the 2 groups are still separable. How can I change the axis scales so I bring the samples in each group closer together? Thank you

The plotPCA function uses ggplot2 to do the plotting, so all you need to do is capture the output in a variable and make changes yourself.

z <- plotPCA(<args go here>)
z + coord_fixed(<xlim and ylim arguments go here>)

There are approximately three gazillion answers to a Google search for 'ggplot change axis' or whatever, or you could look at ?coord_fixed. I find in general that Googling what I want to do with tidyverse stuff is usually much easier than trying to trudge through the documentation or (gasp) trying to read the code to figure out what's up.