weighted unifrac differences

Dear all,

I want to ask what’s the difference between

weighted_unifrac_distance_matrix.qza

and

weighted_unifrac_pcoa_results.qza

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?

Thank you

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 :wink:

Wikipedia can explain more:

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Ok, so with just the PCoA.qza file, we can already plot the data set and use this in R for plotting right? And the distance.qza, is not really needed?

yes

Not for generating PCoA plots, since you already have the PCoA coordinates file.