I suppose the PCOA result is the data of all the plots. But I wondered what’s the purpose of the distance_matrix.qza? And how is this useful, I extracted the file but it doesn’t make sense to me. And what can I do with the datafile with the distance_matrix.qza?
Correct, it gives the PCoA coordinates for each sample
This shows the pairwise distances between each sample. It sounds like you got both of these outputs from the core-metrics-phylogenetic pipeline. The distance matrix is used to calculate the PCoA coordinates — see here for more details on the many steps that pipeline performs.
The distance matrix can also be used for many more actions — because we aren’t just calculating pairwise distances for the sake of PCoA plots. Some examples are given in the flowchart of the tutorial I linked to above, e.g., beta-group-significance.
It doesn’t make sense to most humans! That’s what the computer is there for