cytoscape.js-hierarchical

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cytoscape.js-hierarchical

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A Cytoscape.js extension for the hierarchical clustering algorithm

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cytoscape-hierarchical
================================================================================

![Screenshot of clusters returned from hierarchical clustering algorithm](https://raw.githubusercontent.com/cytoscape/cytoscape.js-hierarchical/master/demo-img.png)

## Description

A hierarchical clustering algorithm for Cytoscape.js.

## Dependencies

* Cytoscape.js >= 2.6.12

## Usage instructions

Download the library:
 * via npm: `npm install cytoscape-hierarchical`,
 * via bower: `bower install cytoscape-hierarchical`, or
 * via direct download in the repository.

`require()` the library as appropriate for your project:

CommonJS:
```js
var cytoscape = require('cytoscape');
var hierarchical = require('cytoscape-hierarchical');

hierarchical( cytoscape ); // register extension
```

AMD:
```js
require(['cytoscape', 'cytoscape-hierarchical'], function( cytoscape, hierarchical ){
  hierarchical( cytoscape ); // register extension
});
```

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

## API

#### Mode 1: "regular"
Under the ```regular``` mode, the algorithm returns an array of clusters generated from the data set.
One may set the ```threshold``` option to specify a stopping point for the algorithm.
When every cluster is more than ```threshold``` distance apart, clustering is stopped and the current set of hierarchies is returned.

```js
cy.elements().hierarchical({
    mode: "regular",                    // extension mode
    threshold: 25,                      // stopping criterion that affects granularity (#) of clusters

distance: "euclidean",              // distance metric for measuring the distance between two nodes
    linkage: "single",                  // linkage criteria for determining the distance between two clusters
    attributes: [                       // attributes/features used to group nodes
        function(node) {
          return node.position('x');
        },
        function(node) {
          return node.position('y');
        }
    ]
});
```

#### Mode 2: "dendrogram"
Under the ```dendrogram``` mode, the algorithm returns an array of clusters generated from the data set, and generates a dendrogram of the clusters.
One may set the ```cutoff``` option to specify the level at which the tree is cut. This option partitions clusters at different precisions.
For example, in the demo img above, setting ```cutoff = 2``` will return the clusters {D,F,E}, {C}, {A}, {B}. Setting ```cutoff = 1``` will return the clusters {D,F,E,C}, {A,B}. Setting ```cutoff = 0``` will return a single cluster containing all the nodes.

Since the ```dendrogram``` mode generates many additional nodes and edges in order to render the tree, it might not be performant for large data sets. Thus it is recommended to use ```regular``` mode for clustering instead.

```js
cy.elements().hierarchical({
    mode: "dendrogram",                 // extension mode
    cutoff: 2,                          // stopping criterion that affects granularity (#) of clusters

```demo.html``` provides working examples of the 2 different modes using separate data sets.

##### Linkage Types
```average``` - the distance between two clusters is an average of the differences between the nodes in the clusters.

```single``` - the distance between clusters is the smallest distance between a node from each cluster.

```complete``` - the distance between clusters is the largest distance between two nodes in the clusters.

## 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`
1. Publish: `gulp publish`
1. If publishing to bower for the first time, you'll need to run `bower register cytoscape-hierarchical https://github.com/cytoscape.js-hierarchical.git`

cytoscape.js-hierarchical

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