I'm analyzing my HTseq count data using DEseq2 package. I generated the PCA plot using

plotPCA(rld, intgroup="condition")

Is there any straightforward way to label the points in a PCA plot by the names of the samples? (for example using a value named "sampleNames").

Thanks in advance!

If there is an easy way, I am sure Mike will be along soon with whatever that might be. For now, do note that plotPCA uses ggplot2, so you can always capture the output and rejigger to your heart's content. Using the example for plotPCA, we can do this:

> example(plotPCA)
## now recapture the last plot in a variable
> z <- plotPCA( DESeqTransform( se ) )
## replot, obscuring points with the sample name
> z + geom_label(aes(label = name))
## or 'nudge' the points up a bit
> nudge <- position_nudge(y = 1)
> z + geom_label(aes(label = name), position = nudge)
## different label without the box action
> z + geom_text(aes(label = name), position = nudge)

I am a big fan of the geom_label_repel, that you can also find directly implemented in the pcaplot function in my package, pcaExplorer (http://bioconductor.org/packages/pcaExplorer/) - note that you would need the ggrepel package