Hi again @Sparkle,
The visualizers you are using in gneiss are actually deprecated... when running them or reading the help docs you should see this note:
This command is deprecated and will be removed in a future version of this plugin.
So just beware that you are using a visualizer that the developers plan to remove in the next release of gneiss. The developer of gneiss, @mortonjt, now favors his newer method, songbird, so you may want to try that out instead:
Because that ASV is only classified to the family level, so gneiss is being nice and showing you the terminal taxonomic label.
Not in an easy way — you could use python to customize the labels easily enough but there is no way to modify these labels in QIIME 2. collapsing will NOT work.
Yep, collapsing creates a new feature table where the IDs = the shared taxonomy. So you lose the ASV-level information for running gneiss (bad) and cannot relate that information back to the original gneiss you ran (also bad).
So I'm sorry I can't give a better answer! It really boils down to this: you want a customized output and are running up against the technical capabilities of gneiss and QIIME 2... you need to work out a custom solution to an individualized need
This could be called a feature request too... but gneiss visualizers have been deprecated so you should probably start switching over to songbird instead.