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https://github.com/iVis-at-Bilkent/cytoscape.js-cise

An implementation of the circular layout algorithm by Dogrusoz et al. as a Cytoscape.js extension
https://github.com/iVis-at-Bilkent/cytoscape.js-cise

graph-algorithms graph-drawing graphviz

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An implementation of the circular layout algorithm by Dogrusoz et al. as a Cytoscape.js extension

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README 

        
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](http://cs.bilkent.edu.tr/~ivis/) 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](https://dlnext.acm.org/doi/abs/10.1109/TVCG.2012.178)" 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.](https://www.youtube.com/watch?v=SMDAQajK-E8)



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:



```js

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



for(var i = 0; i



```



## API



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

 

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



```js

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](https://github.com/iVis-at-Bilkent/cytoscape.js-layout-utilities#default-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`

1. Commit the build : `git commit -am "Build for release"`

1. Bump the version number and tag: `npm version major|minor|patch`

1. Push to origin: `git push && git push --tags`

1. Publish to npm: `npm publish .`

1. 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`

1. [Make a new release](https://github.com/iVis-at-Bilkent/cytoscape.js-cise/releases/new) for Zenodo.



## Team



  * [H. Eren Calik](https://github.com/herencalik), [Ugur Dogrusoz](https://github.com/ugurdogrusoz) of [i-Vis at Bilkent University](http://www.cs.bilkent.edu.tr/~ivis)



### Alumni



  * [Alihan Okka](https://github.com/alihanokka)