Firstly, thank you for the tutorial on qiime2R. It has been a life saver.
However, I am currently struggling to do beta diversity analysis specifically creating a Bay Curtis distance table based PCoA graph and colring one of my columns.( e.g. how do I get the How do I code for that? I have all my required metadata files along with my .qza files from qiime2. I am trying to do 16S data analysis.
Welcome to the forums! 
Here's how I would build a PCoA plot using qiime2R and Phyloseq.
Import my data into a Phyloseq object using qiime2R::qza_to_phyloseq()
Plot an ordination, like PCoA, using phyloseq::plot_ordination().
You may have found these already, but the Phyloseq tutorials are awesome! They cover how to do what you are asking and have lots of great examples.
- Basics
- Workflows
- Graphics
- Differential Abundance
EDIT: I declined your other post because it's pretty similar to this one. We will read your question, you don't have to post twice!
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