Hi! I've analysed the same data in a few different ways and I've generated pcoa plots for each method. I'm just trying to see if there's any way I can compare the pcoa plots, or if there is a way I can combine the data matrices for each plot and run something similar to make_emperor.py on qiime2?
Yes, the analogous is to use these two commands:
qiime diversity procrustes-analysis ...
qiime emperor procrustes-plot ...
Also, in QIIME2 I would use Mantel's test between the two originating distance matrices to asses the fit between the distances. To do this you would use qiime diversity mantel.
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