phylovega 0.3
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Description:
phylovega 0.3
PhyloVega
Visualize phylogenetic trees in Vega from Python.
Declarative tree visualizations in Python powered by Vega.
Declarative Grammar
from phylovega import TreeChart
# Construct Vega Specification
chart = TreeChart.read_newick(
'tree.newick',
height_scale=200,
# Node attributes
node_size=200,
node_color="#ccc",
# Leaf attributes
leaf_labels="id",
# Edge attributes
edge_width=2,
edge_color="#000",
)
chart.display()
Interactive trees
Use Vega grammar
How does it work?
PhyloVega defines a Vega grammar (specifically, a set of transforms) to draw phylogenetic trees.
Why?
Python is due for a simple, interactive phylogenetic tree viewer. Vega has done
most of the heavy lifting here. PhyloVega simply leverages Vega transform specifications for building interactive visualizations.
In the works
Here is a list of features that will eventually make it into PhyloVega.
More Interactivity
Collapible Clades.
Circular trees
... (feel free to add to this list).
Install
Get the latest release with pip:
pip install phylovega
Install the development version by cloning this repo and calling:
pip install -e .
Dependencies
PhyloVega uses the Vega4 specification. It works out-of-the-box with JupyterLab.
JupyterLab: The next generation Jupyter notebook.
PhyloPandas: Pandas DataFrame for Phylogenetics
License:
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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