DeepPhe-Viz-v2

January 13, 2026 · View on GitHub

A visualization platform for DeepPhe cancer phenotype data.

Project Overview

DeepPhe-Viz is a web-based application designed to visualize and interact with cancer phenotype data processed by the DeepPhe system. It provides researchers and clinicians with an intuitive interface to explore complex datasets, facilitating better understanding and analysis of cancer phenotypes.

Features

📊 Interactive data visualization
🔍 Advanced filtering and search
💾 Direct SQLite database access (no IndexedDB)
🚀 Optimized performance with caching
📱 Responsive design
🔒 Secure deployment options

Development

Prerequisites

Node.js (v18.x or higher)
npm (v8.x or higher)
Modern web browser (Chrome, Firefox, Edge recommended)

Installation

Clone the repository:

git clone https://github.com/DeepPhe/DeepPhe-Viz-v2.git
cd DeepPhe-Viz-v2

Install dependencies:

npm install

Start the development server:

npm start

Visit http://localhost:3000/ to see the visualization.
To stop the server, press Ctrl + C in the terminal.

Production Deployment

🐳 Docker Deployment (Recommended)

# Build and run with Docker Compose
docker-compose up -d

# View logs
docker-compose logs -f

# Stop the application
docker-compose down

Your app will be running at: http://localhost:3000 (or your server IP:3000)

🔧 Manual Docker Commands

# Build the Docker image
docker build -t deepphe-visualizer .

# Run the container
docker run -d -p 3000:3000 --name deepphe-viz deepphe-visualizer

# View logs
docker logs -f deepphe-viz

# Stop and remove
docker stop deepphe-viz && docker rm deepphe-viz

Build for Production

npm run build

This creates an optimized production build in the build/ directory.

Project Structure

Viz2/
├── public/                 # Static files
│   └── demopatients.sqlite # SQLite database
├── src/
│   ├── components/         # React components
│   ├── utils/
│   │   └── db/
│   │       └── sqlite_client.js  # SQLite database client
│   └── App.js
├── build/                  # Production build (generated)
├── server.js               # Express server
├── Dockerfile              # Docker configuration
└── docker-compose.yml      # Docker Compose setup

Database

The application uses SQLite for data storage:

File: demopatients.sqlite
Location: public/ directory
Access: Direct SQL queries via sql.js

Testing

# Run unit tests
npm test

# Run SQLite client tests
npm test -- sqlite_client.test.js

Scripts

Command	Description
`npm start`	Start development server
`npm run build`	Build for production
`npm test`	Run tests

Environment Variables

Create a .env file for custom configuration:

PORT=3000
NODE_ENV=production

Browser Support

Chrome (latest)
Firefox (latest)
Safari (latest)
Edge (latest)

License

See LICENSE file for details.

Contributing

Fork the repository
Create a feature branch
Make your changes
Run tests
Submit a pull request