PCoA from q1 and q2 otu table


I have never worked in qiime one and recently started to figure out how to work with q2.

I have a dataset analysed in qiime2, but now I need to compare it to the analysis of the same data done with qiime1 by my colleague (who is not accessible at the moment). from q1 analysis I have normalized OTU table at the moment (I may request any intermediate for the analysis files, but that may take some time to get).

the question - is it possible to get PCoA plot from the merged OTU table from different analysis? If yes, then how can I do it?

so far I realise that to run PCoA I would need to create a tree and a table artifacts. is it a must?

I see that I could merge the two OTU tables based on phylogeny assignment and do some PCoA but in R, for example.
any thoughts and help will be highly appreciated. I am quite inexperienced user, so I apologize if I did not describe the problem that well.

Thank you!

Hi @rakshy!

To make sure I understand, do you have a QIIME 1 table, which you'd like to merge with a QIIME 2 table? Or is it that you want to contrast the QIIME 1 table against the QIIME 2 table by looking at two PCoA plots?

If it's the former case (merging these two tables), then we'll need to know what kind of OTU picking was performed. For example, if it was closed-reference, then the taxonomy/phylogeny is already known via the reference, and there's a couple strategies for merging.

If it's the latter case (you just want to contrast the two PCoA plots), then you shouldn't need any additional data, but it will depend on the kind of metric you are trying to use. From what you've described you have only the OTU table at this point (no phylogeny) correct?

You should be able to run core-metrics on that table (you'll need to import it first with a command like this), since it does not require a phylogeny like core-metrics-phylogenetic does.

Alternatively, you can compute any (non-phylogenetic) metric you feel like with a sequence of:

  1. qiime diversity beta
  2. qiime diversity pcoa
  3. qiime emperor plot

Let me know if that all makes sense.

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