top taxa vs top phyla/genera/species; some insights?

[SoilRotifer (Mike Robeson)]

Hi @MarwaTawfik,

This might be related to the issue discussed in this thread:

Mismatch between qiime2 taxa bar plot and phyloseq taxa bar plot

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(…

-Mike