Hi @Sam_Degregori,
We are missing some information on the QIIME 2 side, prior to making the taxonomy plot:
- What filtering was performed?
- Were the data rarefied ?
- Were unwanted taxa removed?
- That is, did you perform the same operations in QIIME 2 as you did in phyloseq? If not, you are truely comparing apples to oranges here.
Within R / phyloseq there are several operations that may be contributing to the observed differences:
You've:
- rarefied the data :
rarefy_even_depth(im) - ran
tax_glom(im,taxrank=“Phylum”)w/o settingNArm=False- This is likely the biggest issue. Any taxa with 'NA' in the column 'Phylum' (i.e. missing taxonomy for that rank) will be discarded unless you set this to
False. Default isTrue. Check the help text for this.
- This is likely the biggest issue. Any taxa with 'NA' in the column 'Phylum' (i.e. missing taxonomy for that rank) will be discarded unless you set this to
- Finally you are removing low count reads:
filter_taxa(imP, function(x) sum(x > 0) > (0.000001*length(x)), TRUE)
-I hope this helps! 
-Mike