plot-phylo
Python package to plot a phylogenetic tree on an existing matplotlib axis.
Science Score: 67.0%
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✓DOI references
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○Scientific vocabulary similarity
Low similarity (19.5%) to scientific vocabulary
Repository
Python package to plot a phylogenetic tree on an existing matplotlib axis.
Basic Info
- Host: GitHub
- Owner: KatyBrown
- License: mit
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://plot-phylo.readthedocs.io
- Size: 68.9 MB
Statistics
- Stars: 23
- Watchers: 1
- Forks: 1
- Open Issues: 6
- Releases: 10
Metadata Files
README.md
plot_phylo
This module allows the user to plot a phylogenetic tree on an existing matplotlib axis.
This means that: * Phylogenies can be incorporated into existing plots. * Annotations can be added using standard matplotlib functionality. * Plots can be output in png, pdf, svg or tiff formats. * Automatically generated and updated figures can include phylogenies
Full documentation is available via ReadTheDocs.
The module depends on the ETE Toolkit, an excellent existing Python framework for analysing and visualising phylogenetic trees, plus the matplotlib visualisation library. It is designed to make generating complex figures incorporating phylogenies easier, as matplotlib plotting functions can be used on top of the basic tree.
Installation
Requirements
- python >= 3.6
- matplotlib >= 2.1.1
- ete3 >= 3.1.0
The module can be installed using pip
pip install plot_phylo
You can also download the latest release here
Or clone the GitHub repository directly.
git clone git@github.com:KatyBrown/plot_phylo.git
Quick Start
For detailed usage instructions, visit our ReadTheDocs page.
To draw a phylogeny under the default settings onto a blank figure.
``` import matplotlib.pyplot as plt import plot_phylo
Create an empty plot, 8in (width) by 10in (height) - matplotlib
f = plt.figure(figsize=(8, 10))
Add an axis - matplotlib
ax = plt.subplot()
Plot the tree on this axis, using the default settings - plot_phylo
results = plotphylo.plotphylo("examples/primates.nw", ax)
Save the tree - matplotlib
plt.savefig("examples/basicplot.png", bboxinches='tight') ```
Cite
If you use this repository in your work, please cite:
Brown, K (2024) plotphylo. https://github.com/KatyBrown/plotphylo
Continuous Integration
I use GitHub Actions for continuous integration to ensure code quality. You can view the configuration here.
Owner
- Name: Katy Brown
- Login: KatyBrown
- Kind: user
- Location: University of Cambridge
- Twitter: thekatybrown1
- Repositories: 7
- Profile: https://github.com/KatyBrown
Citation (citation.cff)
cff-version: 1.2.0
message: "If you use this repository in your work, please cite:"
authors:
- family-names: Brown
given-names: Katy
orcid: 0000-0002-8400-6922
title: "plot_phylo"
version: v0.0.11
identifiers:
- type: doi
value: https://doi.org/10.5281/zenodo.13871592
date-released: 2024-10-01
url: "https://github.com/KatyBrown/plot_phylo"
GitHub Events
Total
- Create event: 2
- Issues event: 2
- Release event: 2
- Watch event: 8
- Push event: 24
- Pull request event: 3
- Fork event: 1
Last Year
- Create event: 2
- Issues event: 2
- Release event: 2
- Watch event: 8
- Push event: 24
- Pull request event: 3
- Fork event: 1
Packages
- Total packages: 1
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Total downloads:
- pypi 90 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 12
- Total maintainers: 1
pypi.org: plot-phylo
This module allows the user to plot a phylogenetic tree on an existing matplotlib axis.
- Homepage: https://github.com/KatyBrown/plot_phylo
- Documentation: https://plot-phylo.readthedocs.io
- License: MIT License
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Latest release: 1.0.1
published 7 months ago
Rankings
Maintainers (1)
Dependencies
- ete3 *
- matplotlib *
- actions/checkout v2 composite
- actions/setup-python v2 composite