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24.0 6.0 4.0 1.68 MB

Jupyter lab widget for rendering graphs (networks)

TypeScript 6.19% CSS 0.51% Jupyter Notebook 93.30%

cy-jupyterlab's Introduction

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)

© 2022 University of California, San Diego

Trey Ideker Lab

cy-jupyterlab's People

Contributors

Stargazers

Watchers

Forkers

bodom0015 fernandomora itunderscore tmtabor

cy-jupyterlab's Issues

[Wrong data is referenced as a NetworkName]

When we import the cx data from NDEX, wrong point of data is referenced as a NetworkName.
The code of catching NetworkName is below.
https://github.com/idekerlab/cy-jupyterlab/blob/5b512c3d6bbe162d61a485e3457e8e44fdefc2db/src/index.tsx#L74

NPM Release

The last NPM release was 5 years ago. When will the new version from a few months ago get pushed to NPM?

Javascript Error: o.cyNetworkUtils is not a constructor

Hi cy team! Thank you for the great tool!

I'm trying to use cy-jupyterlab example on JupyterLab 1.1.4 and I've faced with the error Javascript Error: o.cyNetworkUtils is not a constructor:

Please help me to fix it. Thanks!

[Python Cell] It doesn't catch the size of output window of notebook's cell.

When use cy-jupuyterlab on python's cell like example, the graph is not drawn on center and the button is disabled.
Maybe the Cytoscape.js doesn't catch the size of window at the beginning.
After we change the browser window size, we can use the command.

ReactElement type error?

when i follow the installation instructions, an error occurs in npm run build:

$ npm run build

> [email protected] build /Users/jamesanderson/jupyter/cy-jupyterlab
> tsc

node_modules/@types/react-transition-group/TransitionGroup.d.ts:16:30 - error TS2314: Generic type 'ReactElement<P>' requires 1 type argument(s).

16         childFactory?(child: ReactElement): ReactElement;

this, with [email protected] and [email protected]

Does cy-jupyterlab have any facility for editing the graph

Does cy-jupyterlab have any facility for editing the graph and returning the graph to python code in the jupyterlab notebook?

cy-jupyterlab appears to be designed to view graphs - but not to edit them - is that correct?

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