cytoscape/cy-jupyterlab

Jupyter lab widget for rendering graphs (networks)

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.
• Automatic layouts

Requirments

• JupyterLab - Tested on v3.4

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:

jlpm install
jlpm build
jupyter labextension link .

To rebuild the package and the JupyterLab app:

jlpm 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)

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© 2022 University of California, San Diego

Trey Ideker Lab