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

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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.