How to add dots to the PCA (in addition to labels)?

Question

[tanya_fiskur]

I made a PCA plot after RUVseq normalization with the command

plotPCA(threeset, col=colors[threex], cex=1.2)

The resulting plot is a bit unreadable. How can I add the dots (and remain labels), or at least do the plot in dots, and put labels into legend? It looks like this now: https://ibb.co/0nqfmc9 Thanks a lot in advance!

Answer 1

[Kevin Blighe]

Hey Tanya,

Looks like you're using prcomp() to perform PCA?

You can re-use some of the code that I posted here: A: PCA plot from read count matrix from RNA-Seq

Or, there is also a dedicated package that I developed: PCAtools: everything Principal Component Analysis

Kevin