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toytree

A minimalist tree plotting library using toyplot graphs

https://github.com/eaton-lab/toytree

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    5 of 19 committers (26.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.9%) to scientific vocabulary

Keywords

phylogeny plotting python tree

Keywords from Contributors

genomics assembly rad-seq bioinformatics genotype-phenotype-maps
Last synced: 6 months ago · JSON representation

Repository

A minimalist tree plotting library using toyplot graphs

Basic Info
  • Host: GitHub
  • Owner: eaton-lab
  • License: bsd-3-clause
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage: http://eaton-lab.org/toytree
  • Size: 23.5 MB
Statistics
  • Stars: 176
  • Watchers: 7
  • Forks: 29
  • Open Issues: 16
  • Releases: 6
Topics
phylogeny plotting python tree
Created almost 9 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

Toytree

Tree plotting with Toytree in Python

Welcome to toytree, a Python library for tree object data parsing, visualization, manipulation, and numerical and evolutionary analyses. If you are new to toytree, head to the User Guide to see examples and learn about its features.

The goal of toytree is to provide a light-weight Python equivalent to widely used tree analysis and plotting libraries in R, and in doing so, to promote further development of phylogenetic and evolutionary analysis methods in Python.

Toytree generates rich interactive figures (SVG+HTML+JS) that render in jupyter-notebooks or webpages, and can be exported as high quality SVG, PDF, or PNG figures for publications. The library is minimal dependencies, is easy to install, and can be easily incorporated into other projects.

Current release info

| Name | Downloads | Version | Platforms | | --- | --- | --- | --- | | Conda Recipe | Conda Downloads | Conda Version | Conda Platforms |

Installing toytree

Toytree can be installed using conda or pip (conda preferred): conda install toytree -c conda-forge It is possible to list all of the versions of toytree available on your platform with: conda search toytree --channel conda-forge

Documentation

See the full documentation at http://eaton-lab.org/toytree.

Example code

```python

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('~prz') rtre.draw(width=400, tiplabelsalign=True);

or chain a few functions together

tre.root('~prz').drop_tips("~tham").ladderize().draw();

extensive styling options are available

rtre.draw( tiplabelscolors='pink', nodelabels='support', nodesizes=15, nodecolors="cyan", edgestyle={ "stroke": "darkgrey", "stroke-width": 3, }, ) ```

Example plots

./manuscript/ToyTree-figure.svg

Owner

  • Name: Eaton Lab
  • Login: eaton-lab
  • Kind: user
  • Location: NYC

The Eaton Lab at Columbia University

GitHub Events

Total
  • Create event: 5
  • Release event: 4
  • Issues event: 7
  • Watch event: 13
  • Delete event: 1
  • Member event: 1
  • Issue comment event: 6
  • Push event: 75
  • Pull request review event: 2
  • Pull request event: 9
  • Fork event: 2
Last Year
  • Create event: 5
  • Release event: 4
  • Issues event: 7
  • Watch event: 13
  • Delete event: 1
  • Member event: 1
  • Issue comment event: 6
  • Push event: 75
  • Pull request review event: 2
  • Pull request event: 9
  • Fork event: 2

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 1,605
  • Total Committers: 19
  • Avg Commits per committer: 84.474
  • Development Distribution Score (DDS): 0.17
Past Year
  • Commits: 173
  • Committers: 4
  • Avg Commits per committer: 43.25
  • Development Distribution Score (DDS): 0.214
Top Committers
Name Email Commits
Deren d****6@c****u 1,332
deren d****n@y****u 184
natetrux n****x@g****m 32
smau8 s****4@c****u 19
Isaac Overcast i****t@g****m 7
Kinggerm c****r@f****m 7
Patrick McKenzie p****e@c****u 6
Russell Neches r****l@v****g 3
Rahim16 r****m@m****i 2
Zachary Sailer z****r@g****m 2
aalsabag a****g@g****m 2
cactuskid d****i@u****h 2
Carlos Alonso c****l@g****m 1
Colin Dewey c****y@w****u 1
SimonGreenhill S****l 1
Patrick Franklin McKenzie p****9@h****r 1
Fishlab f****b@F****l 1
Fishlab f****b@F****l 1
The Gitter Badger b****r@g****m 1
Committer Domains (Top 20 + Academic)
columbia.edu: 3 gitter.im: 1 fishlabs-mini.wireless.yale.internal: 1 holmes.cm.cluster: 1 wisc.edu: 1 unil.ch: 1 mamed.li: 1 vort.org: 1 foxmail.com: 1 yale.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 61
  • Total pull requests: 45
  • Average time to close issues: 4 months
  • Average time to close pull requests: 25 days
  • Total issue authors: 34
  • Total pull request authors: 16
  • Average comments per issue: 1.28
  • Average comments per pull request: 0.6
  • Merged pull requests: 36
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 13
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 6 days
  • Issue authors: 4
  • Pull request authors: 2
  • Average comments per issue: 1.25
  • Average comments per pull request: 0.54
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • eaton-lab (14)
  • isaacovercast (6)
  • dereneaton (3)
  • MauriAndresMU1313 (3)
  • isgilman (2)
  • StuntsPT (2)
  • pmckenz1 (2)
  • ryneches (2)
  • cndewey (2)
  • Markkunitomi (1)
  • ilevantis (1)
  • aleferna12 (1)
  • chtate (1)
  • Flying-Doggy (1)
  • bede (1)
Pull Request Authors
  • natetrux (33)
  • pmckenz1 (4)
  • Zsailer (4)
  • ryneches (4)
  • Kinggerm (3)
  • smau8 (2)
  • hackers-test (2)
  • isaacovercast (2)
  • eaton-lab (2)
  • gitter-badger (1)
  • aalsabag (1)
  • camayal (1)
  • Rahim16 (1)
  • SimonGreenhill (1)
  • cactuskid (1)
Top Labels
Issue Labels
bug (6) enhancement (3) help wanted (2)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 8
    (may contain duplicates)
  • Total versions: 9
  • Total maintainers: 1
conda-forge.org: toytree

A simple library for tree visualization, manipulation, and evolutionary analysis in Python.

  • Versions: 8
  • Dependent Packages: 1
  • Dependent Repositories: 8
Rankings
Dependent repos count: 12.1%
Average: 26.2%
Dependent packages count: 29.0%
Stargazers count: 30.3%
Forks count: 33.6%
Last synced: 6 months ago
spack.io: py-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.

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Average: 28.5%
Dependent packages count: 57.0%
Maintainers (1)
snehring
Last synced: 6 months ago

Dependencies

.github/workflows/demo.yml actions
  • actions/checkout v2 composite
docs/requirements.txt pypi
  • ipykernel *
  • nbsphinx *
  • scipy *
  • sphinx >=1.4
  • sphinx_rtd_theme *
setup.py pypi
  • future *
  • numpy *
  • requests *
  • toyplot *
binder/environment.yml conda
  • python >=3
  • toytree