Hi I performed a PCoA from a distance matrix provided by Mash. The issue is that now I need to add environmental metadata fitted to the PCoA.
The source data that I have is a genomic distance matrix provided by Mash software and environmental metadata in a table.
my professor recommended me to use Ampvis2 package for performing an ordination and adding a envfit() function to the ordination. The issue is that for creating an ampvis2 object I should provide a OTU table and then perform the ordination.
I was reading the "Using a custom distance matrix" part of this documentation https://madsalbertsen.github.io/ampvis2/reference/amp_ordinate.html#using-a-custom-distance-matrix-1 but I still need to provide a OTU table for creating a ampvis2 object.
So what is the way on which I can perform a biplot only having a genomic distance matrix plus environmental metadata in R?
