Is it possible to get a bray-curtis distance matrix output from the analysis and not just the PCoA plot?
I was attempting ways to get the artifact visualized other than the plot, but maybe I am missing something simple I can’t find on the website.
The UniFrac Distance boxplots could be helpful but it only lets me use my other metadata category and not compare sample-sample.
Is there a way to get that distance matrix output other than PCoA plots and for there to be a sample-sample comparison, not just my metadata category for the diversity plugin?
I might be misunderstanding your question, but yes, there are a few ways to grab the Bray-Curtis Distance Matrix! If you ran core-metrics, this is one of the outputs (here is an example from the Moving Pictures Tutorial). You could choose to export that, if you had some downstream analysis/visualization you wished to run.
Are you reference to an analysis like beta-group-significance? If you, I’m not sure what is to be gained with performing this kind of sample-to-sample comparison, because all the “groups” will be unique, which means that there will be no computable “within” distances.