Construction of dendrogram using pre-calculated distance-matrix.tsv/.qza?

Hi all! I have a pre-calculated jaccard distance-matrix.tsv file that I want to be reconstructed into dendrogram. I'm wondering if there's a qiime2 command for me to make the distance-matrix.tsv or qza file input into a dendrogram clustering? Thanks a lot!

Hi @rmbn, unfortunately I don't know of any visualizations in the QIIME 2 core distribution that do that (there is a feature-table heatmap function does something similar, but it doesn't accept distance matrices). Your best be is to export and generate the plot in the tool of your choice. Keep us posted! :qiime2:

Hello @thermokarst! Thanks for the response. I was able to use PHYLIP (Trex-online) with just a little tweaking on the distance matrix format compatible for PHYLIP.

I was also able to create one using qiime diversity beta-rarefaction. I was just wondering if the metrices in this command is just the same as the one in qiime diversity core-metrics-phylogenetic pipeline because I want my data (distance matrix) to be consistent with the tree. I found out that qiime diversity beta-rarefaction has default iteration value of 10 and since this is done randomly, it may provide different values from all other computation and is may not the exact reflection of my computed metrics from qiime diversity core-metrics-phylogenetic. The .qzv files from qiime diversity beta-rarefaction do not have the distance matrix file (and it shows slightly different PCoA plots from the ones in qiime diversity core-metrics-phylogenetic).

While I'm at it, I hope in the future we can include dendrograms outputs for beta diversity metrics in qiime diversity core-metrics-phylogenetic consistent with the distance matrix file it produces. It's easier [for beginners like me] to visualize relationship between samples in clusters like dendrogram. :smiley:

That is actually a plot of many distance matrices, at one single rarefaction depth, which is computed by performing a Mantel test against those many matrices - that doesn't sound like what you were asking for above, so my apologies for not suggesting it. If that gets you what you need, great!

Sort of, but not exactly - rarefaction is a random process, each time you rarefy you will get slightly different results. This visualization summarizes those differences. So you're not really looking at a heatmap of your jaccard distances - you're looking at a heatmap of how those jaccard distances changed (or stayed the same) across multiple rarefaction trials, and the dendrogram is computed for those changes, not for the distance metric.

I hope that helps! :qiime2:

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