Hi @Benedict,
Hmm, just to clarify, did you run relative-frequency on your feature table and the output did not come out as relative abundance? If so, this is odd, would you mind sharing your feature table and the exact commands that you used so we can see if there's any issues?
Or are you saying that the script worked but you are just looking for the taxonomic assignments instead of the feature IDs? If your feature table was the output from Dada2/deblur, then you do not have taxonomic assignments but rather the feature IDs for those sequence variants. When you run taxa barplot you provide this feature table + your taxonomy assignments separately to create a new visualizer, but your original feature table still only has the feature IDs. To create a new feature-table which has taxonomic assignments instead of the feature IDs, you'll want to use the taxa collapse command first. This creates a new feature table with taxonomy collapsed at whatever level you want (i.e 6 for genus), then you can run relative-frequency to convert this new frequency table to relative abundance table. That should give you the output you're looking for.
Edit: If you want this new feature table in a new format, lets say a .tsv format, check out this post with more instructions.
Filtering based on percentages is not currently available in qiime2 yet but is on the radar of the development team (open issue). You can currently either filter based on frequency or see this post for an alternative solution within qiime2.
Hope this helps!