cy-jupyterlab

cy-jupyterlab

A Jupyter Lab extension for interactive graph (network) data visualization

Introduction

Cy-JupyterLab is a Jupyter Lab extension for interactive graph visualization. Current version supports the following data types:

• Cytoscape eXchange format (.cx)
• Cytoscape.js JSON (.cyjs)

Features

• Interactive network visualization in Panels.
• Supports visualization in Jupyter Notebook cells
• Full support for Cytoscape.js compatible styles
• Support for data from NDEx) database.
• Simple node/edge property panel
  • Display filename, number of nodes and edges (elements) in graph
• Automatic layouts

Requirments

• JupyterLab - Tested on v0.34.10

Optional

• ndex2 - this is a python library to import data from NDEx. If you want to use NDEx data sets, this provides high-level API to access the data

Installation

v0.1.0

jupyter labextension install @iau/cy-jupyterlab

v0.5.0 and later (Not released yet)

jupyter labextension install cy-jupyterlab

For Developers

To build the extension from the source, please do the following in the cloned directory:

npm install
npm run build
jupyter labextension link .

To rebuild the package and the JupyterLab app:

npm run build
jupyter lab build

Acknoowledgment

The prototype was developed by the following students as a summer project 2018:

• Hideki Akazawa (University of Osaka, Japan)
• Kaito Uemura (University of Osaka, Japan)

© 2018 University of California, San Diego

Trey Ideker Lab