cytoscape-cise

Description

CiSE(Circular Spring Embedder) is an algorithm based on the traditional force-directed layout scheme with extensions to move and rotate nodes in the same cluster as a group. Further local improvements may be obtained by flipping clusters and by swapping neighboring node pairs in the same cluster, reducing the edge crossing number.

The algorithm is implemented as a Cytoscape.js extension by i-Vis Lab in Bilkent University. Here is a demo:

Please cite the following when using this layout:

M. Belviranli, A. Dilek and U. Dogrusoz, "CiSE: A Circular Spring Embedder Layout Algorithm" in IEEE Transactions on Visualization & Computer Graphics, vol. 19, no. 06, pp. 953-966, 2013.

A detailed illustration of CiSE can also be found here.

In cases where there is no domain-specific way to cluster graphs, Markov Clustering in the Cytoscape.js core library may be used for clustering, based solely on the topology of the graph. You need to set the "clusterID" of the nodes according to their clusters and create an array of arrays where each array is a cluster that contains node IDs. For example:

let clusters = window.cy.elements().markovClustering( options );

for(var i = 0; i<clusters.length; i++){
  for(var j = 0; j<clusters[i].length; j++){
    clusters[i][j]._private.data.clusterID = i;
  }
}

let arrayOfClusterArrays;
window.cy.nodes().forEach(function (node) {
 let clusterID = node.data('clusterID');
 if (uniqueClusterIDs.includes(clusterID)) {
   if(arrayOfClusterArrays[clusterID] == undefined){
     arrayOfClusterArrays[clusterID] = [];
   }
   else{
     arrayOfClusterArrays[clusterID].push(node.data('id'));
   }
 }
 else {
   arrayOfClusterArrays.push([node.data('id')]);
 }
 
var layout = window.cy.layout({name: 'cise',clusters: arrayOfClusterArrays});

Dependencies

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

Optional Dependencies

• cytoscape-layout-utilities: ^1.0.0 (only needed if packComponents is true)

Usage instructions

Download the library:

• via npm: npm install cytoscape-cise,
• via bower: bower install cytoscape-cise, 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 cise from 'cytoscape-cise';

cytoscape.use( cise );

CommonJS require:

let cytoscape = require('cytoscape');
let cise = require('cytoscape-cise');

cytoscape.use( cise ); // register extension

AMD:

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

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

<script src="https://unpkg.com/layout-base/layout-base.js"></script>
<script src="https://unpkg.com/avsdf-base/avsdf-base.js"></script>
<script src="https://unpkg.com/cose-base/cose-base.js"></script>
<script src="https://unpkg.com/cytoscape-cise/cytoscape-cise.js"></script>

API

The following options are supported when calling the layout, e.g,

cy.layout({ name: 'cise', clusters: clusterInfo, ... }):

var default = {
    // -------- Mandatory parameters --------
    name : 'cise',
    
    // ClusterInfo can be a 2D array contaning node id's or a function that returns cluster ids. 
    // For the 2D array option, the index of the array indicates the cluster ID for all elements in 
    // the collection at that index. Unclustered nodes must NOT be present in this array of clusters.
    // 
    // For the function, it would be given a Cytoscape node and it is expected to return a cluster id  
    // corresponding to that node. Returning negative numbers, null or undefined is fine for unclustered
    // nodes.  
    // e.g
    // Array:                                     OR          function(node){ ...
    //  [ ['n1','n2','n3'],                                     return "1";    // or any cluster ID assosiated with node
    //    ['n5','n6']                                           return node.data("clusterID"); // If the cluster IDs are stored in Data element of nodes
    //    ['n7', 'n8', 'n9', 'n10'] ]                         ... }
    clusters: clusterInfo,                                    
                                                              
    
    // -------- Optional parameters --------
    
    // Use random node positions at beginning of layout
    // if this is set to false, the layout will be incremental
    randomize: true, 

    // Whether to animate the layout
    // - true : Animate while the layout is running
    // - false : Just show the end result
    // - 'end' : Animate directly to the end result
    animate: false,
    
    // number of ticks per frame; higher is faster but more jerky
    refresh: 10, 
    
    // Animation duration used for animate:'end'
    animationDuration: undefined,
    
    // Easing for animate:'end'
    animationEasing: undefined,
    
    // Whether to fit the viewport to the repositioned graph
    // true : Fits at end of layout for animate:false or animate:'end'
    fit: true,
    
    // Padding in rendered co-ordinates around the layout
    padding: 30,

    // Whether to include labels in node dimensions
    nodeDimensionsIncludeLabels: false,
    
    // separation amount between nodes in a cluster
    // note: increasing this amount will also increase the simulation time 
    nodeSeparation: 12.5,
    
    // Inter-cluster edge length factor 
    // (2.0 means inter-cluster edges should be twice as long as intra-cluster edges)
    idealInterClusterEdgeLengthCoefficient: 1.4,

    // Whether to pull on-circle nodes inside of the circle
    allowNodesInsideCircle: false,
    
    // Max percentage of the nodes in a circle that can move inside the circle
    maxRatioOfNodesInsideCircle: 0.1,
    
    // - Lower values give looser springs
    // - Higher values give tighter springs
    springCoeff: edge => 0.45,
    
    // Node repulsion (non overlapping) multiplier
    nodeRepulsion: node => 4500,
    
    // Gravity force (constant)
    gravity: 0.25,
    
    // Gravity range (constant)
    gravityRange: 3.8, 

    // whether to pack components of the graph, if set to true, you should import cytoscape.js-layout-utilities
    packComponents: false

    // Layout event callbacks; equivalent to `layout.one('layoutready', callback)` for example
    ready: function(){}, // on layoutready
    stop: function(){}, // on layoutstop
}

To be able to use packComponents option, cytoscape-layout-utilities extension should also be registered in the application. Packing related options should be set via cytoscape-layout-utilities extension. If they are not set, CiSE uses default options.

Build targets

• npm run test : Run Mocha tests in ./test
• npm run build : Build ./src/** into cytoscape-cise.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-cise https://github.com/iVis-at-Bilkent/cytoscape.js-cise.git
7. Make a new release for Zenodo.

Team

• H. Eren Calik, Ugur Dogrusoz of i-Vis at Bilkent University

Alumni

• Alihan Okka