QIIME 2 function equivalent to NMDS.py from QIIME 1?

[smreyes (Sarah)]

I’m looking to obtain coordinates for distance metrics so I can plot NMDS in R (rather than using the Emperor plots). It seems like this was available in QIIME 1 with NMDS.py (http://qiime.org/scripts/nmds.html). Has this function been incorporated into QIIME 2? If not, is there another way of getting this information?

[Nicholas_Bokulich]

Hi @smreyes,
We have an open issue to add NMDS to QIIME 2 but I do not have an eta for when we can get that added. We will reply here when that method is added.

For now, you will need to export your distance matrix and use QIIME 1 or R to calculate NMDS coordinates… but then you can import back to QIIME 2 (or use standalone emperor) to make emperor plots if that is your preferred visualization method.

Thank you!