I am wondering if it is possible to add in the emperor command line a flag for --n_taxa_to_keep as qiime1. That flag is very useful to visualize which OTUs are influencing more. Also, is there a way to rarefy the beta diversity as before with multiple_rarefactions_even_depth.py and represents that on 2D/3D?
For extra stats in beta diversity (adonis, anosim, db_RDA), I will need to use vegan and ape in R as in qiime1. However, please do you know how I can get those files from qiime2 compatible with R? In the same way otu_table, tax_table, and phylogenetic tree files for R phyloseq.
In (un)weighted-unifrac-treatment-significance.qzv (picture), I think in the second plot, distance to T1 from T1 should be 0, also the number of replicates is multiply for the n in the first plot. I don’t know if this is fix in qiime2-2017.12.
So sorry about so many questions, and many thanks in advance!!