I created a PCoA on weighted UniFrac distance and felt that it would be useful to find the loadings of the PCoA axes. I might want to find which features are taking higher weights along a specific axis. Does anyone know how to check the loadings?
Unfortunately with principal coordinates analysis there’s no way to access loading information (as in principal component analysis). Recall that PCoA is computed based on a distance matrix, and distance functions preserve no information about the features that make up the distances.
Another alternative would be to use something like EMDUniFrac. Based on UniFrac distances, it can tell you about discriminant branches in your tree (paper).