Strange! In my own work with Phyloseq it’s been very flexible with both data structures and plot color schemes.
Another option is to use psmelt() first to turn your phyloseq object in a traditional data frame, then modify and graph using tidyverse and ggplot2. We can explore this option more, because we know psmelt() and the tidyverse packages seem to be working.
Want to try that?
ahh okay… I can try that! It’s probably likely I am doing something wrong as I am only getting started 
I did something similar to what you have suggested 
but by downloading the .tsv file directly off of the relative abundance bar plots (the .qzv file) from QIIME2 . Bit of a cheat but it gives me the data in the arrangement I need. As you recommended, I then used tidyverse and ggplot2 from the tutorial. I appreciate all your advice and help with this!
2 posts were split to a new topic: how to get a phyloseq object with qiime2r?