# clld-phylogeny-plugin
Plugin for the [clld](https://github.com/clld/clld) framework providing
support for phylogenetic trees in clld apps.
This plugin includes the [phylotree](https://github.com/veg/phylotree.js/tree/master)
library to render phylogenetic trees in the browser.
[](https://github.com/clld/clld-phylogeny-plugin/actions?query=workflow%3Atests)
[](https://pypi.python.org/pypi/clld-phylogeny-plugin)
## Introduction
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](https://github.com/clld/clld-phylogeny-plugin/blob/master/src/clld_phylogeny_plugin/models.py) to store phylogenetic trees (and how the tree labels correspond to `Language` objects)
- adding a [`Tree` component](https://github.com/clld/clld-phylogeny-plugin/blob/f98e83681e7464d3abfb05eae2f1a3c74fdabc1f/src/clld_phylogeny_plugin/tree.py#L34), 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.
## Usage
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`:
```python
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.
### Plotting parameters on trees
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:
```python
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)
```
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"description": "# clld-phylogeny-plugin\n\nPlugin for the [clld](https://github.com/clld/clld) framework providing\nsupport for phylogenetic trees in clld apps.\n\nThis plugin includes the [phylotree](https://github.com/veg/phylotree.js/tree/master)\nlibrary to render phylogenetic trees in the browser.\n\n[](https://github.com/clld/clld-phylogeny-plugin/actions?query=workflow%3Atests)\n[](https://pypi.python.org/pypi/clld-phylogeny-plugin)\n\n\n## Introduction\n\nWhile 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.\n\nThe `clld-phylogeny-plugin` package supports this kind of visualization by\n- adding [database models](https://github.com/clld/clld-phylogeny-plugin/blob/master/src/clld_phylogeny_plugin/models.py) to store phylogenetic trees (and how the tree labels correspond to `Language` objects)\n- adding a [`Tree` component](https://github.com/clld/clld-phylogeny-plugin/blob/f98e83681e7464d3abfb05eae2f1a3c74fdabc1f/src/clld_phylogeny_plugin/tree.py#L34), allowing simple rendering of a tree on a page\n- 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.\n\n\n## Usage\n\nTODO: See https://github.com/clld/grambank/commit/4101243597c3c95d21786fe8bdcf8cf060da609b for a minimal example.\n\nTo make `clld-phylogeny-plugin` functionality available to a `clld` app, it must be included in the app's configuration - typically in `<app>:main`:\n```python\n config.include('clld_phylogeny_plugin')\n```\n\nThis will add a *Resource* `Phylogeny` with corresponding routes\n- `/phylogenys` - the index page listing all available phylogenies\n- `/phylogenys/<ID>` - a phylogeny's details page, by default rendering the associated tree.\n\n\n### Plotting parameters on trees\n\nTo synchronize plotting of markers for parameter values on maps and trees, the `Tree.get_marker` method may need to\nbe adjusted. This can be done by registering a derived `Tree` class as `ITree` utility:\n```python\nclass MyTree(clld_phylogeny_plugin.tree.Tree):\n def get_marker(self, valueset):\n # compute marker shape and color from valueset\n return shape, color\n\n....\n config.registry.registerUtility(MyTree, ITree)\n```\n",
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