phylovega 0.3

Interactive Phylogenetic trees in Vega from Python.

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