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# 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](https://plot-phylo.readthedocs.io/en/latest/index.html).
The module depends on the [ETE Toolkit](http://etetoolkit.org/), an excellent existing Python framework for analysing and visualising phylogenetic trees, plus the [matplotlib](https://matplotlib.org/) 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](https://github.com/KatyBrown/plot_phylo/releases/latest)
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](https://plot-phylo.readthedocs.io/en/latest/index.html).
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 = plot_phylo.plot_phylo("examples/primates.nw", ax)
# Save the tree - matplotlib
plt.savefig("examples/basic_plot.png", bbox_inches='tight')
```
## Cite
If you use this repository in your work, please cite:
Brown, K (2024) plot_phylo. https://github.com/KatyBrown/plot_phylo
## Continuous Integration
I use GitHub Actions for continuous integration to ensure code quality. You can view the configuration [here](https://github.com/KatyBrown/plot_phylo/blob/main/.github/workflows/main.yml).
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"description": "<br>\n[](https://plot-phylo.readthedocs.io/en/latest/?badge=latest)<br>\n[](https://www.repostatus.org/#active)<br>\n<br>\n\n\n# plot_phylo\n\n![Illustration](./examples/layered.png \"Illustration\")\n\nThis module allows the user to plot a phylogenetic tree on an existing matplotlib axis.\n\nThis means that:\n* Phylogenies can be incorporated into existing plots.\n* Annotations can be added using standard matplotlib functionality.\n* Plots can be output in png, pdf, svg or tiff formats.\n* Automatically generated and updated figures can include phylogenies\n\nFull documentation is available via [ReadTheDocs](https://plot-phylo.readthedocs.io/en/latest/index.html).\n\nThe module depends on the [ETE Toolkit](http://etetoolkit.org/), an excellent existing Python framework for analysing and visualising phylogenetic trees, plus the [matplotlib](https://matplotlib.org/) 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.\n\n\n## Installation\n\n**Requirements**\n\n* python >= 3.6\n* matplotlib >= 2.1.1\n* ete3 >= 3.1.0\n\nThe module can be installed using pip\n\n`pip install plot_phylo`\n\nYou can also download the latest release [here](https://github.com/KatyBrown/plot_phylo/releases/latest)\n\nOr clone the GitHub repository directly.\n\n`git clone git@github.com:KatyBrown/plot_phylo.git`\n\n## Quick Start\nFor detailed usage instructions, visit our [ReadTheDocs page](https://plot-phylo.readthedocs.io/en/latest/index.html).\n\nTo draw a phylogeny under the default settings onto a blank figure.\n\n```\nimport matplotlib.pyplot as plt\nimport plot_phylo\n\n# Create an empty plot, 8in (width) by 10in (height) - matplotlib\nf = plt.figure(figsize=(8, 10))\n\n# Add an axis - matplotlib\nax = plt.subplot()\n\n# Plot the tree on this axis, using the default settings - plot_phylo\nresults = plot_phylo.plot_phylo(\"examples/primates.nw\", ax)\n\n# Save the tree - matplotlib\nplt.savefig(\"examples/basic_plot.png\", bbox_inches='tight')\n```\n\n\n## Cite\n\nIf you use this repository in your work, please cite:\n\nBrown, K (2024) plot_phylo. https://github.com/KatyBrown/plot_phylo\n\n## Continuous Integration\nI use GitHub Actions for continuous integration to ensure code quality. You can view the configuration [here](https://github.com/KatyBrown/plot_phylo/blob/main/.github/workflows/main.yml).\n",
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