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!!
PCoA biplots are not yet supported in q2-emperor, but we have an open issue here tracking progress on that feature. For now, you should use qiime1 or phyloseq to make biplots. It should be fairly straighforward to export your data from QIIME2 into formats that qiime1 and phyloseq can consume (e.g., biom tables or possibly even distance matrices) — please see the data exporting tutorials for more information. A number of forum posts (e.g., here) have also covered exporting specific data types for use in phyloseq, so searching the forum may assist in this process.
Could you please post your second and third and fourth questions to separate posts? This will make these issues easier to answer and track, and for other users to search for help in the future. Thank you!
Thank you.