Does QIIME2 have ordination plots?

[MADscientist314 (Michael Jochum)]

Hi I'm looking to recreate something like this in the QIIME2 environment instead of using phyloseq in R. Any ideas?
Thanks,
Michael

[Nicholas_Bokulich]

Hi @MADscientist314,
Yes! QIIME 2 does have methods for ordination plots. It does not have NMDS (only PCoA), but Bray-Curtis (as in your example) and a variety of other dissimilarity/distance metrics are available.

See here for an example of using this in a basic workflow — the "emperor" plots are the results you want to check out, and click on the "view" tabs to view interactive ordination plots, e.g., this.

Let us know if that's what you were looking for.