Phylogenetic tree with abundance

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1

Hi there,

I'm doing a metabarcoding analysis of both ITS and 16S targets.
I filtered the feature table to have only the most 50 representative Genera in a not quick way, since I could not extract the rep-sequences from a collapsed table.

Basically, I collapsed the table at the level 6, then looked for the frequencies of the first 50, went back to the original feature table and chose a much lower frequency (because the species when collapsed are less than the expected) to finally have a filtered table with the first 50 taxa. Using this feature table I then extracted the related sequences from the rep-seqs, aligned and created the tree.
I now would like to create a phylo tree with relative abundance among the sample, like the following one, but I have no idea how to do it.
Any help please?
Thanks

genus_100.tree
genus_100.tree1920×1440 166 KB

2

Hello Silvia,

This is a pretty visualization, but in my opinion abundances presented on the tree are not informative.

  • the stacked bars have no counts/relative abundance axis
  • it's really hard to compare bars when they're placed in circular manner.
  • there are too many colors and they repeat.

I strongly encourage you to think about another way to represent ASV abundance data, because this is very hard to interpret.

Best wishes
Valentyn

3

Hi @SilviaT,

One way to get the taxonomy for a specific feature is to follow the procedure here:

Then you can create any array of figures you'd like.

Alternatively, you can try using q2-empress.

-Cheers!