Sounds like you are on your way to coming up with a way to accomplish this visualization outside of QIIME 2, which is what I was going to recommend to you here anyway. What you are trying to view is not supported by QIIME 2 at present, and we don't have plans to implement this in the near future.
Have you had a look at feature-table heatmap? While not UPGMA, this does support clustering on the sample and feature axes, independently. You have the option to annotate metadata, too.
If you have any further questions, I think it would make sense to ask those in a new Topic (or Topics) on the Forum. Thanks!
Great viz! We don’t yet support viewing a phylogenetic tree like this in QIIME 2, but if we did, we would most likely allow for users to provide metadata to annotate the labels with. Since taxonomy is viewable as metadata in QIIME 2, that means you could relabel with taxonomy strings just as easily as any other type of metadata.
Since we don’t support this type of visualization yet, you will need to export your tree and your taxonomy and merge those yourself, possibly with the aid of some tree-viewer program.