PCoA (emperor) on two groups only rather than all groups under one variable/category?

Hi team

I was wondering if I could visualize (PCoA, emperor) only two groups of the same variable (rather than all groups)?
I was advised by Rob Knight to try this for my data and see what I would get. I used nf-core/ampliseq already with its qiime2 workflow. Do I need to run the workflow on the two groups only? can't I click and select the each two groups together?
here a screenshot


emperor.zip (9.7 KB)

Thanks very much
Marwa

Hello!
The option to hide samples from the PCoA plot was mostly implemented for the convinience of data exploration and should not replace data filtering.
Please check how to filter distance matrix based on the metadata.
You can use filtered matrix to create new PCoA visualization since PCoA plot coordinates of each sample are recalculated after filtering.

Best,

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