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https://github.com/moshi4/phytreeviz

Simple phylogenetic tree visualization python package for phylogenetic analysis
https://github.com/moshi4/phytreeviz

bioinformatics biopython matplotlib phylogenetic-trees python visualization

Last synced: 4 days ago
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Simple phylogenetic tree visualization python package for phylogenetic analysis

Host: GitHub
URL: https://github.com/moshi4/phytreeviz
Owner: moshi4
License: mit
Created: 2023-09-07T09:15:13.000Z (about 1 year ago)
Default Branch: main
Last Pushed: 2024-09-14T02:59:31.000Z (2 months ago)
Last Synced: 2024-09-14T15:58:29.218Z (2 months ago)
Topics: bioinformatics, biopython, matplotlib, phylogenetic-trees, python, visualization
Language: Python
Homepage: https://moshi4.github.io/phyTreeViz/
Size: 2.34 MB
Stars: 37
Watchers: 2
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff

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README

        # phyTreeViz

![Python3](https://img.shields.io/badge/Language-Python3-steelblue)

![OS](https://img.shields.io/badge/OS-_Windows_|_Mac_|_Linux-steelblue)

![License](https://img.shields.io/badge/License-MIT-steelblue)

[![Latest PyPI version](https://img.shields.io/pypi/v/phytreeviz.svg)](https://pypi.python.org/pypi/phytreeviz)

[![conda-forge](https://img.shields.io/conda/vn/conda-forge/phytreeviz.svg?color=green)](https://anaconda.org/conda-forge/phytreeviz)

[![CI](https://github.com/moshi4/phyTreeViz/actions/workflows/ci.yml/badge.svg)](https://github.com/moshi4/phyTreeViz/actions/workflows/ci.yml)

## Table of contents

- [Overview](#overview)

- [Installation](#installation)

- [API Usage](#api-usage)

- [CLI Usage](#cli-usage)

## Overview

phyTreeViz is a simple and minimal phylogenetic tree visualization python package implemented based on matplotlib.

This package was developed to enhance phylogenetic tree visualization functionality of BioPython.

phyTreeViz is intended to provide a simple and easy-to-use phylogenetic tree visualization function without complexity.

Therefore, if you need complex tree annotations, I recommend using [ete](https://github.com/etetoolkit/ete) or [ggtree](https://github.com/YuLab-SMU/ggtree).

## Installation

`Python 3.8 or later` is required for installation.

**Install PyPI package:**

    pip install phytreeviz

**Install conda-forge package:**

    conda install -c conda-forge phytreeviz

## API Usage

Only simple example usage is described in this section.

For more details, please see [Getting Started](https://moshi4.github.io/phyTreeViz/getting_started/) and [API Docs](https://moshi4.github.io/phyTreeViz/api-docs/treeviz/).

### API Example

#### API Example 1

```python

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")

tv = TreeViz(tree_file)

tv.show_branch_length(color="red")

tv.show_confidence(color="blue")

tv.show_scale_bar()

tv.savefig("api_example01.png", dpi=300)

```

![example01.png](https://raw.githubusercontent.com/moshi4/phyTreeViz/main/docs/images/api_example01.png)  

#### API Example 2

```python

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")

tv = TreeViz(tree_file, height=0.7)

tv.show_scale_axis()

tv.set_node_label_props("Homo_sapiens", color="grey")

tv.set_node_label_props("Pongo_abelii", color="green", style="italic")

tv.set_node_line_props(["Hylobates_moloch", "Nomascus_leucogenys"], color="orange", lw=2)

tv.set_node_line_props(["Homo_sapiens", "Pan_troglodytes", "Pan_paniscus"], color="magenta", ls="dotted")

tv.savefig("api_example02.png", dpi=300)

```

![example02.png](https://raw.githubusercontent.com/moshi4/phyTreeViz/main/docs/images/api_example02.png)  

#### API Example 3

```python

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")

tv = TreeViz(tree_file, align_leaf_label=True)

tv.show_scale_axis()

group1 = ["Hylobates_moloch", "Nomascus_leucogenys"]

group2 = ["Homo_sapiens", "Pan_paniscus"]

tv.highlight(group1, "orange")

tv.highlight(group2, "lime")

tv.annotate(group1, "group1")

tv.annotate(group2, "group2")

tv.marker(group1, marker="s", color="blue")

tv.marker(group2, marker="D", color="purple", descendent=True)

tv.marker("Pongo_abelii", color="red")

tv.savefig("api_example03.png", dpi=300)

```

![example03.png](https://raw.githubusercontent.com/moshi4/phyTreeViz/main/docs/images/api_example03.png)  

#### API Example 4

```python

from phytreeviz import TreeViz, load_example_tree_file

from matplotlib.patches import Patch

tree_file = load_example_tree_file("medium_example.nwk")

tv = TreeViz(tree_file, height=0.3, align_leaf_label=True, leaf_label_size=10)

tv.show_scale_bar()

group1 = ["Hylobates_moloch", "Nomascus_leucogenys"]

group2 = ["Homo_sapiens", "Pongo_abelii"]

group3 = ["Piliocolobus_tephrosceles", "Rhinopithecus_bieti"]

group4 = ["Chlorocebus_sabaeus", "Papio_anubis"]

tv.highlight(group1, "orange", area="full")

tv.highlight(group2, "skyblue", area="full")

tv.highlight(group3, "lime", area="full")

tv.highlight(group4, "pink", area="full")

tv.link(group3, group4, connectionstyle="arc3,rad=0.2")

fig = tv.plotfig()

_ = fig.legend(

    handles=[

        Patch(label="group1", color="orange"),

        Patch(label="group2", color="skyblue"),

        Patch(label="group3", color="lime"),

        Patch(label="group4", color="pink"),

    ],

    frameon=False,

    bbox_to_anchor=(0.3, 0.3),

    loc="center",

    ncols=2,

)

fig.savefig("api_example04.png", dpi=300)

```

![example04.png](https://raw.githubusercontent.com/moshi4/phyTreeViz/main/docs/images/api_example04.png)  

## CLI Usage

phyTreeViz provides simple phylogenetic tree visualization CLI.

### Basic Command

    phytreeviz -i [Tree file or text] -o [Tree visualization file]

### Options

    General Options:

      -i IN, --intree IN      Input phylogenetic tree file or text

      -o OUT, --outfile OUT   Output phylogenetic tree plot file [*.png|*.jpg|*.svg|*.pdf]

      --format                Input phylogenetic tree format (Default: 'newick')

      -v, --version           Print version information

      -h, --help              Show this help message and exit

    Figure Appearence Options:

      --fig_height            Figure height per leaf node of tree (Default: 0.5)

      --fig_width             Figure width (Default: 8.0)

      --leaf_label_size       Leaf label size (Default: 12)

      --ignore_branch_length  Ignore branch length for plotting tree (Default: OFF)

      --align_leaf_label      Align leaf label position (Default: OFF)

      --show_branch_length    Show branch length (Default: OFF)

      --show_confidence       Show confidence (Default: OFF)

      --dpi                   Figure DPI (Default: 300)

    Available Tree Format: ['newick', 'phyloxml', 'nexus', 'nexml', 'cdao']

### CLI Example

Click [here](https://github.com/moshi4/phyTreeViz/raw/main/example/example.zip) to download example tree files.  

#### CLI Example 1

    phytreeviz -i "((A,B),((C,D),(E,(F,G))));" -o cli_example01.png

![example01.png](https://raw.githubusercontent.com/moshi4/phyTreeViz/main/docs/images/cli_example01.png)  

#### CLI Example 2

    phytreeviz -i ./example/small_example.nwk -o cli_example02.png \

               --show_branch_length --show_confidence

![example02.png](https://raw.githubusercontent.com/moshi4/phyTreeViz/main/docs/images/cli_example02.png)  

#### CLI Example 3

    phytreeviz -i ./example/medium_example.nwk -o cli_example03.png \

               --fig_height 0.3 --align_leaf_label 

![example03.png](https://raw.githubusercontent.com/moshi4/phyTreeViz/main/docs/images/cli_example03.png)