DESeq2 plotPCA combine replicates

[Michael Love]

hi id0,

There is a collapseReplicates() function in DESeq2 if you want to combine technical replicates.

... and you could create a new DESeqDataSet with this just for plotting.

[dpryan]

As it performs a PCA, that wouldn't really be possible.

[id0]

By default, the plotPCA function in DESeq2 plots the replicates separately. Is there a way to combine replicates so that there is only one dot per group? There does not seem a built-in option for that and it's not obvious to me by looking at the source.