Beta diversity in R - what to export

[Nicholas_Bokulich]

@colinbrislawn

Maybe someone could suggest a Qiime API tutorial to get you started!

If all you want to do is generate a heatmap, this can be achieved with a few lines in python. See here:

Phylogenetic distance and differences in microbiome

QIIME 2 does not have a method for making distance heatmaps. If you are proficient with python, you could view as a heatmap easily with scikit-bio. Something like this: import qiime2 import skbio dm = qiime2.Artifact.load(distance-matrix.qza).view(skbio.DistanceMatrix) dm [the output of dm will be a distance matrix heatmap]