Newick Tree Visualizer

A tool for creating interactive visualizations of phylogenetic trees in Newick format.

⭐ Support the Project

If you find this project helpful, please consider giving it a star on GitHub! It helps make the project more visible and encourages further development.

✨ Features

• 🌳 Interactive visualization of phylogenetic trees
• 🎨 Configurable node and branch styling
• 🎯 Custom grouping and coloring of nodes
• 📐 Multiple layout directions (right, left, up, down)
• 🔄 Draggable nodes for manual layout adjustments
• 💾 Multiple export formats (HTML, PNG, JPG, PDF)
• ⚡️ Support for large-scale trees
• 🎯 Optional confidence values display

📦 Installation

System Dependencies

Google Chrome is required:

# macOS
brew install --cask google-chrome

# Ubuntu
sudo apt-get update
sudo apt-get install google-chrome-stable

# CentOS
sudo yum install google-chrome-stable

Python Package

pip install newick-visualizer

🚀 Quick Start

Basic Usage

newick-viz input.nwk groups.json -o output.html

Example with Options

newick-viz input.nwk groups.json \
    -o output.jpg \
    --padding 21 \
    --points 8 \
    --distance-threshold 1.5 \
    --min-branch-length 35 \
    --default-length 60 \
    --max-branch-length 80 \
    --opacity 0.6 \
    --font-size 13 \
    --font-weight bold \
    --link-width 3.0 \
    --link-color '#f7cc4f' \
    --render-delay 2000

Export Formats

Supports multiple output formats:

# Interactive HTML
newick-viz input.nwk groups.json -o tree.html

# Static Images
newick-viz input.nwk groups.json -o tree.jpg
newick-viz input.nwk groups.json -o tree.png

# PDF Document
newick-viz input.nwk groups.json -o tree.pdf

🎮 Interactive Features

🖱️ Node Dragging

• Click and drag any node to manually adjust its position
• Connected lines and group backgrounds will update automatically
• Visual feedback during dragging (node highlight and size change)
• Changes persist in the visualization

↩️ Undo Function

• Undo button available in the top-left corner
• Reverts the last node movement
• Multiple levels of undo supported
• Visual feedback when undo is available/unavailable
• Keyboard shortcut support (⌃/⌘ + Z)

✨ Hover Effects

• Nodes enlarge slightly on hover
• Labels become more prominent
• Smooth transitions for all visual changes

🛠️ Configuration Options

Basic Options

• -o, --output: Output file path [default: tree_visualization.html]
• --render-delay: Rendering delay in milliseconds [default: 2000]

Visual Style

• --padding: Padding around nodes in pixels [default: 35]
• --opacity: Opacity of group backgrounds (0-1) [default: 0.3]
• --points: Number of points around each node [range: 6-24] [default: 12]
• --distance-threshold: Distance threshold for group backgrounds [default: 1.2]

Font Settings

• --font-size: Font size in pixels [default: 12]
• --font-family: Font family [default: "Arial, sans-serif"]
• --font-weight: Font weight [default: "normal"]

Branch Settings

• --min-branch-length: Minimum branch length [default: 30]
• --max-branch-length: Maximum branch length [default: 70]
• --default-length: Default length when no confidence value [default: 40]

Connection Line Style

• --link-color: Color of connecting lines [default: "#999999"]
• --link-width: Width of connecting lines [default: 1.5]

Other Settings

• --show-confidence: Show confidence values [flag]

📝 Input File Formats

Newick File

Uses standard Newick format, for example:

((A:0.1,B:0.2)0.95:0.3,C:0.4);

Groups Configuration File (JSON)

{
  "layout": {
    "direction": "right",
    "groupOrder": ["Group1", "Group2"]
  },
  "groups": {
    "Group1": {
      "color": "#ffcdd2",
      "members": ["A", "B"],
      "order": ["B", "A"]
    },
    "Group2": {
      "color": "#c8e6c9",
      "members": ["C"],
      "order": ["C"]
    }
  }
}

🔧 Development Installation

git clone https://github.com/Bengerthelorf/newick-visualizer.git
cd newick-visualizer
pip install -e .

Project Structure

.
├── _version.py
├── LICENSE
├── MANIFEST.in
├── newick_visualizer/
│   ├── __init__.py
│   ├── core/
│   │   ├── tree_generator.py
│   │   ├── template_manager.py
│   │   └── utils.py
│   └── templates/
│       ├── base.html
│       ├── scripts/
│       │   ├── tree.js
│       │   ├── layout.js
│       │   ├── groups.js
│       │   └── main.js
│       └── styles/
│           └── main.css
├── README.md
└── setup.py

🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

1. Fork the repository
2. Create your feature branch: git checkout -b feature/amazing-feature
3. Commit your changes: git commit -m 'Add amazing feature'
4. Push to the branch: git push origin feature/amazing-feature
5. Open a Pull Request

If you have any suggestions or feedback, please submit them on our GitHub Issues page.

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

🙏 Acknowledgments

• D3.js - Visualization library
• Selenium - Automated export generation