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fmarotta / recPhylo

Parse recPhyloXML and phyloXML files in R.
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Rewrite recPhylo in terms of Phylo #3

Closed fmarotta closed 3 months ago

fmarotta commented 3 months ago

Now that we have a Phylo class, we should use it to represent the phylogeny elements of both spTree and recGeneTree, if possible.

fmarotta commented 3 months ago

The primitive entities that we care about are phylogeny and recPhyloXML. A phyloXML is a list of phylogeny and a recPhyloXML is a list of spTree (a simple phylogeny) and recGeneTrees (a list of phylogeny). Besides being made by phylogeny elements, phyloXML and recPhyloXML don't have much in common when it comes to plotting.

The refactor in 796c210 adds functions that work in terms of phylogeny and recPhyloXML. So there is one layout for recPhylo objects and one layout for phylogeny objects.