phytreeviz 0.2.0
Simple phylogenetic tree visualization python package
License: MIT
Requires Python: >=3.8,<4.0
Keywords: bioinformatics,phylogenetics,visualization,matplotlib,phylogenetic-tree

# phyTreeViz

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## 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

## 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)