Here are some selected projects that are compatible with cytoscape: * Dagre layout engine * cola.js graph constraint engine * Vega agraph visualization grammar
There are some great docs - js.cytoscape.org 
# About
Cytoscape.js allows you to easily display and manipulate rich, interactive graphs.
Because Cytoscape.js allows the user to interact with the graph and the library allows the client to hook into user events, Cytoscape.js is easily integrated into your app, especially since Cytoscape.js supports both desktop browsers, like Chrome, and mobile browsers, like on the iPad.
Cytoscape.js includes all the gestures you would expect out-of-the-box, including pinch-to-zoom, box selection, panning, et cetera.
Cytoscape.js also has Graph Analysis in mind: The library contains many useful functions in graph theory. You can use Cytoscape.js headlessly on Node.js to do graph analysis in the terminal or on a web server.
Cytoscape.js is an open-source project, and anyone is free to contribute. For more information, refer to the GitHub README.
The library was developed at the Donnelly Centre at the University of Toronto. It is the successor of Cytoscape Web.
# See also
Vega is a visualization grammar, a declarative format for creating, saving and sharing interactive visualization designs.
It has not really been possible until very recently to represent large interactive graphs visually, and especially not on the web.
Here we look at how we might visualise the Federation, and explore using Cytoscape to achieve a scaleable ability to visualise the network of links and in particular Network of Forks relevant to a particular writing context.
Though Cytoscape.js shares its name with Cytoscape, Cytoscape.js is not exactly the same as Cytoscape desktop. Cytoscape.js is a JavaScript library for programmers. It is not an app for end-users, and developers need to write code around Cytoscape.js to build graphcentric apps.