CYTOSCAPE JS EXAMPLE HOW TO
CYTOSCAPE JS EXAMPLE CODE

The problem, then, is to filter the elements to show only a relevant subset of the graph that a user could easily parse - and to allow the user easy navigation from one chosen subset to another one. An example of a highly-connected hairball Large, highly-connected graphs tend to be more or less a hairball regardless of choice of layout. Choice of layout can help with that issue to some degree. Even assuming that you never have performance issues with large graphs and that you make an ideal choice of layout, large graphs usually just become visual noise. The root issue with large graphs is that it is difficult for a person to visually parse so many data points at once. Consider what questions might be answered for a user with the data, and select subgraphs that can help to answer those questions. It is often a mistake to simply put an entire large dataset in the graph and run a layout on the entire graph. The first step in choosing a layout is choosing the graph or subgraph on which the layout is run. A continuous layout may also support animate: 'end', which animates in a similar manner to a discrete layout: The nodes are animated directly from the start positions to the end positions - avoiding potentially unaesthetic middle iteration positions. This can make a continuous layout give its end result quicker. This makes the layout run all its iterations at once, albeit still asynchronously. Further, a continuous layout may be configured to disable animation via animate: false. If a discrete layout is run as an animation via animate: true, then that layout is no longer synchronous. How animation affects synchronicity An example of an animated layoutĪnimation options can alter the properties of continuous and discrete layouts.

CYTOSCAPE JS EXAMPLE CODE

Instead, you must use events or promises to run code after the layoutstop event. You can not read resultant layout positions for a continuous layout on the line following n(). There is a major distinction between these classes of layouts with respect to synchronicity.Ī discrete layout is synchronous: The resultant positions are synchronously set such that you can access those resultant node positions on the line of code following n().Ī continuous layout is asynchronous: It runs iterations over time, without monopolising the main thread. While a continuous layout is generally more expensive to run as compared to a discrete layout, a continuous layout may give more sophisticated results. This creates a natural animation effect, though the underlying layout algorithm might or might not create a smooth transition between iterations. The nodes are generally organised in a geometric pattern.Ī continuous layout sets node positions over several iterations, typically through a a force-directed algorithm. The nodes go immediately from their previous positions to their resultant layout positions this makes this class of layout relatively cheap to run.

There are two main classes of layout, discrete and continuous.Ī discrete layout sets node positions all at once. Classes of layouts Discrete and continuous layouts By tweaking the layout options for his dataset, you can often get a better visual result than by using the defaults. Other common options allow for setting the resultant node positions using animation. For example, many layouts have options to control how close nodes are to one another. These options allow you to configure how the layout runs by tuning the layout algorithm’s parameters. The set of options differs from layout to layout. Because a layout takes a set of elements as input, a layout can be used on the entire graph or on a subgraph ( cy.layout() versus eles.layout()). For example, many layouts will organise nodes such that each node is in close proximity to its neighbourhood. Passed edges provide the layout with topology that can help to determine where nodes should be placed. Each node that is passed to a layout is positioned by the layout. The set of nodes of edges, or collection, passed to a layout indicates which graph elements should be considered in the layout.

A layout takes as input a set of nodes and edges along with a set of options. Layout definitionĪ layout is simply a mapping function: It maps a node to a position.

CYTOSCAPE JS EXAMPLE HOW TO

This tutorial gives an overview of how to use layouts generally and when each layout is useful specifically. The choice of which particular layout to use is key, but equally important is the choice of how and when to use a layout.Ĭytoscape supports several layouts, and it supports using layouts in several ways. A good layout can give a comprehensive view of the data. One of the first things to decide when visualising a graph is how lay out the nodes on the screen.

Builtin layouts versus external extensions.

Cytoscape js example