Taxonomic tree

[diegozea]

Hi!

First, thank you very much for this package! It has been handy for me.

I think that it would be great to have an integration with Phylo.jl to easily get the common taxonomic tree for a set of taxa as in the NCBI site. That could be really useful for visualization and exploration.

Ideally, this can be a single function, similar to lineage and most probably depending on that, that also accepts stop_at, but that takes a list/set of NCBITaxons. For example:

using NCBITaxonomy

common_tree([ncbi"Bos taurus", ncbi"Mus musculus", ncbi"Homo sapiens"], stop_at=ncbi"Mammalia")

Best regards,

[tpoisot]

Thank you! It's one of the planned features. I think @richardreeve has done the work on Phylo.jl to make it relatively easy to build, and that's definitely on my list.

[tpoisot]

I have made a documentation page with an example - I think it's a good idea, but I would like to think a bit about the best way to express it.

It can be something like

RootedTree(t::Vector{NCBITaxon}) # Or other types from Phylo

Or it can be a convert function. I'm unsure about the API. @richardreeve and @mkborregaard do you have preferences?

This will be a post v0.1.0 addition anyways, since I have modified the package a bit to make it faster.

[tpoisot]

@diegozea here is the use-case with Phylo.jl : http://docs.ecojulia.org/NCBITaxonomy.jl/dev/phylo/ -- I'm happy to keep thinking about how we can make the process efficient (and this will likely involve some performance improvements in lineage, which is not super fast now).

[diegozea]

Thanks! That example is really useful :)

One thing; do you know why the tips are not being shown? I believe it is a problem with the plot recipe, as getleafnames(tree) works perfectly in that example.

[mkborregaard]

do you know why the tips are not being shown?

There seems to be a bug in the plot recipe. It must be due to changes in Plots, as this did work earlier. Could you open a Phylo issue for it?