Phylogenetic tree visualization

Question

[M.]

Hi,

I have some pyhlogentic trees for 5 proteins and a species tree. I extracted protein counts per species from those protein trees (kinda did a mapping with species and protein counts in trees for those species). It's in this dataframe format:

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Now I need to visualize this data. I need to show this together with the species tree (its in newick format). I want to see tree topology and this data together and it should be searchable at the same time. For example, when I search for "Intoshia_linei_1819745" I should be able to see how many XPA or other proteins are there for Intoshia linei. Can I do this with ete3? Or any other suggestions?

Thanks in advance.

Answer 1

[cfos4698]

I don't quite understand your last point about being able to search the tree topology and find the protein information, at least not after it's been visualised. For tree visualisation along with associated information, I tend to find ggtree (which is R-based, not python) the best. Check chapter 7 here: https://yulab-smu.top/treedata-book/chapter7.html, and this related question: Add metadata based on tree structure.

[M.]

Thanks a lot! It's a quite big tree and I want to reach the visualized data easily. Thats what I was trying to say. Thank you.