I would like to create confidence ellipses around my treatment groups in a Jaccard emperor plot, which I know is possible in phyloseq, but was wondering if this is possible in qiime2? If not, what is the easiest way of getting the qza file to phyloseq to do the analysis? I see conflicting answers on the internet for this.
If you are referring to confidence intervals for the sequencing depth variation, then you can use
qiime diversity beta-rarefaction. For sample-wise variation between groups we don’t have this implemented in Emperor.
We have an open issue in our tracker here but no defined timeline for solving this.
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