I need to render 2D PCoA plots with confidence ellipsoids. After going through help forum posts here I found others looking to do the same and roadmap plans from 2017 to add this functionality--it seemed that this had been added. I generated a jackknifed Emperor plot using "qiime diversity beta-rarefaction", which I had hoped would have confidence ellipsoids, but it did not, so I exported the data from this visualization.qzv file using "qiime tools export" and then tried to render the 2D plot using qiime1's "make_2d_plots.py". I got an error message about the script not being able to guess the format for the file "rarefaction-iteration-correlation.tsv'".
Earlier I was able to get the "make_2d_plots.py" script create 2D plots from a non-jackknifed PCoA using "qiime diversity pcoa" and exporting the data to an "ordination.txt" file.
Is there some further preprocessing necessary to do on the jackknifed exported qiime2 output before qiime1 can make a plot?
I have seen 2D PCoA plots with confidence ellipsoids from papers that used qiime2 (see attached image). Am I missing something?