Species tree view of gene families

[fabsta]

Input: set of gene names, species tree? Internally:

• fetch species absence/presence vector for each gene
• prune species tree or dim leaves with no genes
• schematically draw genes using different colors and directions Output:

[emepyc]

Interesting for a theme.

• fetch species absence/presence vector for each gene This is easy. I have some code to do this (remember the "orthologues tree" theme). I used this presence/absence to use a different color for the absent tree paths (and leaves).
• prune species tree or dim leaves with no genes In this case we can leave them in the tree (using a faded-out color or something like this). If pruning the tree is better, we can use a combination of "get_all_leaves" with "subtree" to get the pruned tree.
• schematically draw genes using different colors and directions This is interesting. It was far more difficult with the previous code, but now that we have "tracks" we can create a new type "arrow" or something like that. It would be more difficult to align the arrows because each track is independent, but we may find a way of displaying this.