PhyloVega

Visualize phylogenetic trees in Vega from Python.

Declarative tree visualizations in Python powered by Vega.

Warning: This package is still under development. Things may still change rapidly.

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",
)

Interactive trees

Use Vega grammar

How does it work?

PhyloVega defines uses Vega grammar to draw phylogenetic trees. It accepts a PhyloPandas DataFrame as input and returns a Vega specification in JSON.

Why?

Python is due for a simple, interactive phylogenetic tree viewer. Vega has done most of the heavy lifting here. PhyloVega simply leverages Vega and gets simple interactivity for free!

In the works

Here is a list of features that will eventually make it into PhyloVega.

Interactive!
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 Vega3 specification. To use in the jupyter notebook, you must install the following Python dependencies.

PhyloPandas: Pandas DataFrame for Phylogenetics
ipyvega: IPython/Jupyter notebook module for Vega and Vega-Lite (a visualization grammar).

jharman25 / phylovega