Plugin for the clld framework providing support for phylogenetic trees in clld apps.

This plugin includes the phylotree library to render phylogenetic trees in the browser.

While plotting cross-linguistic data on a map serves as quick visualization of the correlation between the data and geography, plotting the data on a phylogenetic tree allows inspection of the correlation between the data and some theory about language relatedness, embodied in the tree.

The clld-phylogeny-plugin package supports this kind of visualization by

• adding database models to store phylogenetic trees (and how the tree labels correspond to Language objects)
• adding a Tree component, allowing simple rendering of a tree on a page
• adding support for "plotting" Parameter objects on a tree, i.e. plotting the value for a given (Parameter, Language) pair next to the language's label on the tree.

TODO: See https://github.com/clld/grambank/commit/4101243597c3c95d21786fe8bdcf8cf060da609b for a minimal example.

To make clld-phylogeny-plugin functionality available to a clld app, it must be included in the app's configuration - typically in <app>:main:

    config.include('clld_phylogeny_plugin')

This will add a Resource Phylogeny with corresponding routes

• /phylogenys - the index page listing all available phylogenies
• /phylogenys/<ID> - a phylogeny's details page, by default rendering the associated tree.

To synchronize plotting of markers for parameter values on maps and trees, the Tree.get_marker method may need to be adjusted. This can be done by registering a derived Tree class as ITree utility:

class MyTree(clld_phylogeny_plugin.tree.Tree):
    def get_marker(self, valueset):
        # compute marker shape and color from valueset
        return shape, color
....
    config.registry.registerUtility(MyTree, ITree)