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?
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.
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