alex-treebeard / toytree

A minimalist tree plotting library using toyplot graphs

Toytree

Tree plotting with Toytree

Welcome to toytree, a minimalist tree manipulation and plotting library for use inside jupyter notebooks. Toytree combines a popular tree data structure based on the ete3 library with modern plotting tools based on the toyplot plotting library. The goal of toytree is to provide a light-weight Python equivalent to commonly used tree manipulation and plotting libraries in R, and in doing so, to promote further development of phylogenetic methods in Python. Toytree generates rich interactive figures (SVG+HTML+JS) that can be embedded in jupyter-notebooks or webpages, or rendered in SVG, PDF, or PNG for publications.

Examples Gallery

See the Cookbook section in the documentation

Installation

You can install toytree and its dependencies (toyplot and numpy) with a single command using conda (preferred), or from pip.

conda install toytree -c eaton-lab

Documentation

See the full documentation to see all of the options that toytree provides. Try it out instantly in the cloud using the toytree binder.

Examples

# import toyplot and load a newick file from a public URL
import toytree
tre = toytree.tree("https://eaton-lab.org/data/Cyathophora.tre")

# root the tree using a wildcard string matching and draw a tree figure.
rtre = tre.root(wildcard='prz')
rtre.draw(width=400, tip_labels_align=True);

# or chain a few functions together
tre.root(wildcard='prz').drop_tips(wildcard="tham").ladderize().draw();

# extensive styling options are available
rtre.draw(
    tip_labels_color='pink',
    node_labels='support',
    node_sizes=15,
    node_colors="cyan",
    edge_style={
        "stroke": "darkgrey",
        "stroke-width": 3,
    },
)