ENH: "Preserve" original node names about q2-fragment-insertion HOT 3 CLOSED

Hi @ChrisKeefe, placed features should have preserved tip names. The reference tree will also contain the tips for the reference as well, for Greengenes this is another ~200k tips using GG identifiers. Would that explain what you're observing?

from q2-fragment-insertion.

OK, the plot thickens. It looks like some of the nodes in this tree have preserved their original feature IDs. In this zoomed-in shot of the same tree, I've got a QIIME 2 feature-id, and the expected coloring and taxonomy information.

Not sure why the behavior is inconsistent, but I'll drop a note in here if I run into a good explanation.

from q2-fragment-insertion.

Absolutely does, thanks @wasade ! So the majority of the feature IDs are coming straight out of Silva, and the coloring in Empress is just getting overwhelmed by uncolored reference features not found in our study data.

Setting Empress's --p-shear-to-feature-metadata flag to true (the default IIRC) trims out the non-study nodes, and takes care of the issue nicely.

from q2-fragment-insertion.