phyTreeViz

Table of contents

• Overview
• Installation
• API 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 or 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 and API Docs.

API Example

API Example 1

```python from phytreeviz import TreeViz, loadexampletree_file

treefile = loadexampletreefile("small_example.nwk")

tv = TreeViz(treefile) tv.showbranchlength(color="red") tv.showconfidence(color="blue") tv.showscalebar()

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

API Example 2

```python from phytreeviz import TreeViz, loadexampletree_file

treefile = loadexampletreefile("small_example.nwk")

tv = TreeViz(treefile, height=0.7) tv.showscale_axis()

tv.setnodelabelprops("Homosapiens", color="grey") tv.setnodelabelprops("Pongoabelii", color="green", style="italic")

tv.setnodelineprops(["Hylobatesmoloch", "Nomascusleucogenys"], color="orange", lw=2) tv.setnodelineprops(["Homosapiens", "Pantroglodytes", "Pan_paniscus"], color="magenta", ls="dotted")

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

API Example 3

```python from phytreeviz import TreeViz, loadexampletree_file

treefile = loadexampletreefile("small_example.nwk")

tv = TreeViz(treefile, alignleaflabel=True) tv.showscale_axis()

group1 = ["Hylobatesmoloch", "Nomascusleucogenys"] group2 = ["Homosapiens", "Panpaniscus"]

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) ```

API Example 4

```python from phytreeviz import TreeViz, loadexampletree_file from matplotlib.patches import Patch

treefile = loadexampletreefile("medium_example.nwk")

tv = TreeViz(treefile, height=0.3, alignleaflabel=True, leaflabelsize=10) tv.showscale_bar()

group1 = ["Hylobatesmoloch", "Nomascusleucogenys"] group2 = ["Homosapiens", "Pongoabelii"] group3 = ["Piliocolobustephrosceles", "Rhinopithecusbieti"] group4 = ["Chlorocebussabaeus", "Papioanubis"]

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, bboxtoanchor=(0.3, 0.3), loc="center", ncols=2, )

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

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 to download example tree files.

CLI Example 1

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

CLI Example 2

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

CLI Example 3

phytreeviz -i ./example/medium_example.nwk -o cli_example03.png \
           --fig_height 0.3 --align_leaf_label