cytoscape

What is cytoscape?

Cytoscape is a graph theory library for visualizing and analyzing networks. It provides a comprehensive set of features for creating, manipulating, and rendering graphs, making it suitable for a wide range of applications from bioinformatics to social network analysis.

What are cytoscape's main functionalities?

Graph Creation

This feature allows you to create a graph with nodes and edges. The code sample demonstrates how to initialize a Cytoscape instance, add elements (nodes and edges), and apply styles and layouts.

const cytoscape = require('cytoscape');
const cy = cytoscape({
  container: document.getElementById('cy'),
  elements: [
    { data: { id: 'a' } },
    { data: { id: 'b' } },
    { data: { id: 'ab', source: 'a', target: 'b' } }
  ],
  style: [
    {
      selector: 'node',
      style: {
        'background-color': '#666',
        'label': 'data(id)'
      }
    },
    {
      selector: 'edge',
      style: {
        'width': 3,
        'line-color': '#ccc'
      }
    }
  ],
  layout: {
    name: 'grid',
    rows: 1
  }
});

Graph Manipulation

This feature allows you to dynamically add and remove elements from the graph. The code sample shows how to add a new node and edge, and how to remove an existing node.

cy.add({ group: 'nodes', data: { id: 'c' } });
cy.add({ group: 'edges', data: { id: 'bc', source: 'b', target: 'c' } });
cy.remove(cy.$('#a'));

Graph Layouts

This feature provides various layout algorithms to arrange the graph elements. The code sample demonstrates how to apply a circular layout to the graph.

cy.layout({ name: 'circle' }).run();

Graph Styling

This feature allows you to style the graph elements. The code sample shows how to change the background color of all nodes to blue.

cy.style().selector('node').style({ 'background-color': 'blue' }).update();

Event Handling

This feature enables event handling for graph elements. The code sample demonstrates how to log a message when a node is tapped.

cy.on('tap', 'node', function(evt){
  var node = evt.target;
  console.log('Tapped ' + node.id());
});

Other packages similar to cytoscape

d3

D3.js is a JavaScript library for producing dynamic, interactive data visualizations in web browsers. It uses HTML, SVG, and CSS. While D3 is more general-purpose and flexible, Cytoscape is specialized for graph theory and network visualization.

vis-network

vis-network is a library to visualize dynamic, interactive networks. It is part of the vis.js suite. Compared to Cytoscape, vis-network is simpler and more lightweight but may lack some of the advanced features and customizability of Cytoscape.

sigma

Sigma is a JavaScript library dedicated to graph drawing. It is designed to display interactive static graphs. Sigma is more focused on performance and rendering large graphs, whereas Cytoscape offers a broader range of features for graph analysis and manipulation.

README

Cytoscape.js

Graph theory (network) library for visualisation and analysis : http://js.cytoscape.org

Description

Cytoscape.js is a fully featured graph theory library. Do you need to model and/or visualise relational data, like biological data or social networks? If so, Cytoscape.js is just what you need.

Cytoscape.js contains a graph theory model and an optional renderer to display interactive graphs. This library was designed to make it as easy as possible for programmers and scientists to use graph theory in their apps, whether it's for server-side analysis in a Node.js app or for a rich user interface.

You can get started with Cytoscape.js with one line:

var cy = cytoscape({ elements: myElements, container: myDiv });

Learn more about the features of Cytoscape.js by reading its documentation.

Documentation

You can find the documentation and downloads on the project website.

Roadmap

Future versions of Cytoscape.js are planned in the milestones of the Github issue tracker. You can use the milestones to see what's currently planned for future releases.

Contributing to Cytoscape.js

Please refer to CONTRIBUTING.md.

Citation

To cite Cytoscape.js in a paper, please cite the Oxford Bioinformatics issue:

Cytoscape.js: a graph theory library for visualisation and analysis

Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD

Bioinformatics (2016) 32 (2): 309-311 first published online September 28, 2015 doi:10.1093/bioinformatics/btv557 (PDF)

PubMed Abstract

Build dependencies

Install node, npm and gulp (optional). Of course, npm install before using gulp or npm run.

Build instructions

Run npm run <target> in the console. The main targets are:

Building:

• build: do all builds of the library (unmin, min, umd)
• build:unmin : do the unminified build with bundled dependencies (for simple html pages, good for novices)
• build:min : do the unminified build with bundled dependencies (for simple html pages, good for novices)
• build:umd : do the umd (cjs/amd/globals) build
• clean : clean the build directory
• docs : build the docs into documentation
• release : build all release artefacts
• watch : automatically build lib for debugging (with sourcemap, no babel, very quick)
  • good for general testing on debug/index.html
  • served on http://localhost:8080 or the first available port thereafter, with livereload on debug/index.html
• watch:babel : automatically build lib for debugging (with sourcemap, with babel, a bit slower)
  • good for testing performance or for testing out of date browsers
  • served on http://localhost:8080 or the first available port thereafter, with livereload on debug/index.html
• watch:umd : automatically build prod umd bundle (no sourcemap, with babel)
  • good for testing cytoscape in another project (with a "cytoscape": "file:./path/to/cytoscape" reference in your project's package.json)
  • no http server
• dist : update the distribution js for npm etc.

Testing:

If the TRAVIS or TEST_BUILD environment variables are defined, then mocha or gulp test will test build/cytoscape.umd.js. Otherwise, the unbundled, unbabelified, raw source is tested. This keeps local tests very quick to run on modern versions of node while ensuring we can test old versions of node as well. The library can be built on node>=6, but it can be tested on node>=0.10.

• test : run the Mocha unit tests
• test:build : run the Mocha unit tests (on a built bundle)
• lint : lint the js sources via eslint
• ci : run tests and linting
• ci:build : run tests and linting (on a built bundle)
• benchmark : run all benchmarks
• benchmark:single : run benchmarks only for the suite specified in benchmark/single
• sniper : runs a biojs sniper server that hosts demos

Release instructions

1. Do each backport patch release before the corresponding current release. This ensures that npm lists the current version as the latest one.
2. Make sure the docs are updated with the list of releases in documentation/md/intro.md
3. Update the VERSION environment variable, e.g. export VERSION=1.2.3
4. Confirm all the tests are passing: npm run test (see also test/index.html for browser testing)
5. Prepare a release: npm run release
6. Review the files that were just built in the previous step. Try out the newly-built docs and demos.
7. Add the the release to git: git add . && git commit -m "Build $VERSION"
8. Update the package version: npm version $VERSION
9. Push the release changes: git push && git push --tags
10. Publish the release to npm: npm publish .
11. Create a release for Zenodo from the latest tag

Tests

Mocha tests are found in the test directory. The tests can be run in the browser or they can be run via Node.js (npm test or mocha).