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 : https://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

Would you like to become a Cytoscape.js contributor? You can contribute in technical roles (e.g. features, testing) or non-technical roles (e.g. documentation, outreach), depending on your interests. Get in touch with us by posting a GitHub discussion.

For the mechanics of contributing a pull request, refer to CONTRIBUTING.md.

Feature releases are made monthly, while patch releases are made weekly. This allows for rapid releases of first- and third-party contributions.

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 and npm. Run npm install before using npm run.

Build instructions

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

Building:

• build: do all builds of the library (umd, min, umd, esm)
• 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
• build:esm : do the esm (ES 2015 modules) build
• clean : clean the build directory
• docs : build the docs into documentation
• release : build all release artifacts
• 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:

The default test scripts run directly agasinst the source code. Tests can alternatively be run on a built bundle. The library can be built on node>=6, but the library's bundle can be tested on node>=0.10.

• test : run all testing & linting
• test:js : run the mocha tests on the public API of the lib (directly on source files)
  • npm run test:js -- -g "my test name" runs tests on only the matching test cases
• test:build : run the mocha tests on the public API of the lib (on a built bundle)
  • npm run build should be run beforehand on a recent version of node
  • npm run test:build -- -g "my test name" runs build tests on only the matching test cases
• test:modules : run unit tests on private, internal API
  • npm run test:modules -- -g "my test name" runs modules tests on only the matching test cases
• lint : lint the js sources via eslint
• benchmark : run all benchmarks
• benchmark:single : run benchmarks only for the suite specified in benchmark/single

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. Confirm all the tests are passing in IE9:
   1. npm run watch:umd
   2. Open an IE9 VM
   3. Open http://yourip:8081/test/ie.html in IE
6. Prepare a release: npm run release
7. Review the files that were just built in the previous step. Try out the newly-built docs and demos.
8. Add the the release to git: git add . && git commit -m "Build $VERSION"
9. Update the package version: npm version $VERSION
10. Push the release changes: git push && git push --tags
11. Publish the release to npm: npm publish .
12. Create a release for Zenodo from the latest tag
13. For feature releases: Create a release announcement on the blog. Share the announcement on mailing lists and social media.

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 run test:js).