cytoscape-cose-bilkent

What is cytoscape-cose-bilkent?

The cytoscape-cose-bilkent npm package is a layout algorithm for Cytoscape.js, a graph theory library. It provides a layout algorithm based on the CoSE (Compound Spring Embedder) model, which is particularly useful for visualizing compound graphs with a hierarchical structure.

What are cytoscape-cose-bilkent's main functionalities?

Basic Layout

This code initializes a Cytoscape instance with a basic graph and applies the CoSE-Bilkent layout algorithm to it.

const cy = cytoscape({
  container: document.getElementById('cy'),
  elements: [
    { data: { id: 'a' } },
    { data: { id: 'b' } },
    { data: { id: 'c' } },
    { data: { id: 'd' } },
    { data: { id: 'e' } },
    { data: { id: 'ab', source: 'a', target: 'b' } },
    { data: { id: 'bc', source: 'b', target: 'c' } },
    { data: { id: 'cd', source: 'c', target: 'd' } },
    { data: { id: 'de', source: 'd', target: 'e' } }
  ],
  layout: {
    name: 'cose-bilkent'
  }
});

Custom Layout Options

This code demonstrates how to customize the CoSE-Bilkent layout options, such as node repulsion, ideal edge length, and animation settings.

const cy = cytoscape({
  container: document.getElementById('cy'),
  elements: [
    { data: { id: 'a' } },
    { data: { id: 'b' } },
    { data: { id: 'c' } },
    { data: { id: 'd' } },
    { data: { id: 'e' } },
    { data: { id: 'ab', source: 'a', target: 'b' } },
    { data: { id: 'bc', source: 'b', target: 'c' } },
    { data: { id: 'cd', source: 'c', target: 'd' } },
    { data: { id: 'de', source: 'd', target: 'e' } }
  ],
  layout: {
    name: 'cose-bilkent',
    nodeRepulsion: 4500,
    idealEdgeLength: 50,
    edgeElasticity: 0.45,
    nestingFactor: 0.1,
    gravity: 0.25,
    numIter: 2500,
    tile: true,
    animate: 'end',
    animationDuration: 1000
  }
});

Compound Graph Layout

This code shows how to use the CoSE-Bilkent layout for a compound graph, where nodes can have parent-child relationships.

const cy = cytoscape({
  container: document.getElementById('cy'),
  elements: [
    { data: { id: 'a' } },
    { data: { id: 'b', parent: 'a' } },
    { data: { id: 'c', parent: 'a' } },
    { data: { id: 'd' } },
    { data: { id: 'e' } },
    { data: { id: 'ab', source: 'a', target: 'b' } },
    { data: { id: 'bc', source: 'b', target: 'c' } },
    { data: { id: 'cd', source: 'c', target: 'd' } },
    { data: { id: 'de', source: 'd', target: 'e' } }
  ],
  layout: {
    name: 'cose-bilkent'
  }
});

Other packages similar to cytoscape-cose-bilkent

cytoscape-dagre

The cytoscape-dagre package provides a layout algorithm based on the Dagre library, which is designed for directed graphs. It is particularly useful for hierarchical layouts and is optimized for performance. Compared to cytoscape-cose-bilkent, it is more suitable for directed acyclic graphs (DAGs).

cytoscape-cola

The cytoscape-cola package integrates the Cola.js layout algorithm with Cytoscape.js. It offers advanced features like constraints and handles large graphs efficiently. Compared to cytoscape-cose-bilkent, it provides more flexibility in terms of layout constraints and is better suited for large-scale graphs.

cytoscape-euler

The cytoscape-euler package provides a layout algorithm based on the force-directed approach. It is designed to produce aesthetically pleasing layouts with good separation of nodes. Compared to cytoscape-cose-bilkent, it focuses more on visual aesthetics and is less specialized for compound graphs.

README

cytoscape-cose-bilkent

Description

The CoSE (Compound Spring Embedder) layout for Cytoscape.js developed by i-Vis Lab in Bilkent University is a spring embedder layout with support for compound graphs (nested structures) and varying (non-uniform) node dimensions. (demo, compound demo)

Please cite the following when using this layout:

U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, "A Layout Algorithm For Undirected Compound Graphs", Information Sciences, 179, pp. 980-994, 2009.

Dependencies

• Cytoscape.js ^3.2.0
• cose-base ^1.0.0

Usage instructions

Download the library:

• via npm: npm install cytoscape-cose-bilkent,
• via bower: bower install cytoscape-cose-bilkent, or
• via direct download in the repository (probably from a tag).

Import the library as appropriate for your project:

ES import:

import cytoscape from 'cytoscape';
import coseBilkent from 'cytoscape-cose-bilkent';

cytoscape.use( coseBilkent );

CommonJS require:

let cytoscape = require('cytoscape');
let coseBilkent = require('cytoscape-cose-bilkent');

cytoscape.use( coseBilkent ); // register extension

AMD:

require(['cytoscape', 'cytoscape-cose-bilkent'], function( cytoscape, coseBilkent ){
  coseBilkent( cytoscape ); // register extension
});

Plain HTML/JS has the extension registered for you automatically, because no require() is needed.

API

When calling the layout, e.g. cy.layout({ name: 'cose-bilkent', ... }), the following options are supported:

var defaultOptions = {
  // Called on `layoutready`
  ready: function () {
  },
  // Called on `layoutstop`
  stop: function () {
  },
  // 'draft', 'default' or 'proof" 
  // - 'draft' fast cooling rate 
  // - 'default' moderate cooling rate 
  // - "proof" slow cooling rate
  quality: 'default',
  // Whether to include labels in node dimensions. Useful for avoiding label overlap
  nodeDimensionsIncludeLabels: false,
  // number of ticks per frame; higher is faster but more jerky
  refresh: 30,
  // Whether to fit the network view after when done
  fit: true,
  // Padding on fit
  padding: 10,
  // Whether to enable incremental mode
  randomize: true,
  // Node repulsion (non overlapping) multiplier
  nodeRepulsion: 4500,
  // Ideal (intra-graph) edge length
  idealEdgeLength: 50,
  // Divisor to compute edge forces
  edgeElasticity: 0.45,
  // Nesting factor (multiplier) to compute ideal edge length for inter-graph edges
  nestingFactor: 0.1,
  // Gravity force (constant)
  gravity: 0.25,
  // Maximum number of iterations to perform
  numIter: 2500,
  // Whether to tile disconnected nodes
  tile: true,
  // Type of layout animation. The option set is {'during', 'end', false}
  animate: 'end',
  // Duration for animate:end
  animationDuration: 500,
  // Amount of vertical space to put between degree zero nodes during tiling (can also be a function)
  tilingPaddingVertical: 10,
  // Amount of horizontal space to put between degree zero nodes during tiling (can also be a function)
  tilingPaddingHorizontal: 10,
  // Gravity range (constant) for compounds
  gravityRangeCompound: 1.5,
  // Gravity force (constant) for compounds
  gravityCompound: 1.0,
  // Gravity range (constant)
  gravityRange: 3.8,
  // Initial cooling factor for incremental layout
  initialEnergyOnIncremental: 0.5
};

Note that this extension supports only relatively modern browsers. Browsers like IE require significant shimming, for example with core-js.

Note that while running Cytoscape.js in headless mode, stylingEnabled option of Cytoscape.js should be set as true because this extension considers node dimensions and some other styling properties.

Build targets

• npm run test : Run Mocha tests in ./test
• npm run build : Build ./src/** into cytoscape-cose-bilkent.js
• npm run watch : Automatically build on changes with live reloading (N.b. you must already have an HTTP server running)
• npm run dev : Automatically build on changes with live reloading with webpack dev server
• npm run lint : Run eslint on the source

N.b. all builds use babel, so modern ES features can be used in the src.

Publishing instructions

This project is set up to automatically be published to npm and bower. To publish:

1. Build the extension : npm run build:release
2. Commit the build : git commit -am "Build for release"
3. Bump the version number and tag: npm version major|minor|patch
4. Push to origin: git push && git push --tags
5. Publish to npm: npm publish .
6. If publishing to bower for the first time, you'll need to run bower register cytoscape-cose-bilkent https://github.com/cytoscape/cytoscape.js-cose-bilkent.git
7. Make a new release for Zenodo.