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 layout for Cytoscape.js by the i-Vis Lab in Bilkent University. 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.

Demos

Click here (simple) or here (compound) for demos

Dependencies

• Cytoscape.js ^2.4.0 || ^3.0.0
• Versions after 2.0.4 are not compatible with versions before Cytoscape.js 3.1.0

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).

require() the library as appropriate for your project:

CommonJS:

var cytoscape = require('cytoscape');
var regCose = require('cytoscape-cose-bilkent');

regCose( cytoscape ); // register extension

AMD:

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

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

Please note that Cytoscape.js rendering option styleEnabled must be true, if layout is running in headless mode.

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 () {
  },
  // 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',
  // 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
};

Publishing instructions

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

1. Set the version number environment variable: export VERSION=1.2.3
2. Publish: gulp publish
3. 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
4. Make a release on GitHub to automatically register a new Zenodo DOI