Counting 2,899 Big Data & Machine Learning Frameworks, Toolsets, and Examples...
Suggestion? Feedback? Tweet @stkim1

Author
Contributors
Last Commit
Apr. 16, 2018
Created
Apr. 10, 2017

Toytree

Join the chat at https://gitter.im/toytree-help/Lobby Install with conda https://travis-ci.org/eaton-lab/toytree.svg?branch=master

Tree plotting with Toytree

Toytree is a Python tree plotting library designed for use inside jupyter notebooks. It was motivated from a desire for a simple tree plotting library with a similar aesthetic to the ape package for R. To parse, represent, and manipulate tree objects Toytree uses a modified (minimal) version of the ete3 library (which we call ete3mini). Toytree is written within the framework of the minimalist plotting library toyplot, which generates rich interactive figures (SVG+HTML+JS) that can be embedded in Jupyter-notebooks or webpages, or rendered in SVG or PDF format for publications.

Installation

You can install toytree and its dependencies (toyplot and numpy) with a single command using conda.

conda install toytree -c eaton-lab

Documentation

See the full documentation. Launch a jupyter-notebook on your machine to try it out for yourself.

Examples

## import the toyplot and toytree modules
import toytree
import toyplot
## load trees from newick str, filepath, or URL
url = "http://eaton-lab.org/data/Vib-Oreino.tre"
path = "./tree.newick"
newick = \
"""(41954_cyathophylloides:0.00008888031167776559,(((32082_przewalskii:
0.00259326350604092027,33588_przewalskii:0.00247133969857381459)100:
0.03587422609749137820,(33413_thamno:0.00565358258838428562,(30556_thamno:
0.00653218253974622003,((40578_rex:0.00335406134690998791,35855_rex:
0.00339963302433546593)100:0.00222999650239191338,(35236_rex:0.00580524693403740473,
(39618_rex:0.00096208118162745867,38362_rex:0.00109218434613194098)100:
0.00617527349892385037)96:0.00073890038051916795)99:0.00078336549990502716)100:
0.00103379657491441167)100:0.00538723112354794632)100:0.00297626149201316807,
(29154_superba:0.00634236826447889986,30686_cyathophylla:0.00669944988923529706)
100:0.00237994755604001816)100:0.00941020878048287081,41478_cyathophylloides:
0.00005282184335845886);"""

## load newick string to create a Toytree class object
tre1 = toytree.tree(url)
tre2 = toytree.tree(path)
tre3 = toytree.tree(newick)

Tree plotting basics

The .draw() function generates a plot that is returned as a tuple containing a toyplot.Canvas object and a toyplot.Canvas.cartesian object. In a jupyter-notebook the canvas will automatically render as HTML in an output cell. Toytree applies a default styling to the tree which can be modified extensively.

canvas, axes = tre3.draw(width=400, node_labels=True)
canvas

Styling options

By default toytree generates figures in HTML following the design ethos of toyplot, which is designed to create figures for the web (though figures can also be saved in common formats like SVG). It uses CSS styling options to modify plot components that will be familiar to users with web-design experience. For advanced usage I recommend becoming more familiar with the Toyplot documentation. The figure below demonstrates several styling options that can be applied to a tree plot.

tre3.draw(
    width=500,
    height=500,
    node_labels=True,
    node_labels_style={
        "font-size": "10px",
        "fill": "white"
        },
    node_size=16,
    node_style={
        "stroke": "green",
        "stroke-width": 2,
        "fill": "#333333",
        "opacity": 0.5,
        },
    tip_labels=True,
    tip_labels_style={
        "font-size": "14px",
        "-toyplot-anchor-shift": "18px",
        "fill": "darkcyan",
        },
    edge_style={
        "stroke": "orange",
        "stroke-opacity": 0.8,
        "stroke-dasharray": "3,3",
        "stroke-width": 3,
        },
    use_edge_lengths=False,
    tree_style="c",
    orient="down",
    );

Latest Releases
0.1.6
 Feb. 1 2018
0.1.5
 Jan. 28 2018
0.1.4
 Sep. 22 2017
0.1.3
 Jun. 15 2017
0.1.2
 Apr. 27 2017