Cytoscape layout algorithms

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This purpose of this page is to discuss Cytoscape Layout Algorithms.

Wikipedia Link about Graph Drawing

Table of Contents Cytoscape Algorithms Force Directed Algorithms Spring Embedded Algorithms JGraph Algorithms yWorks Algorithms

Cytoscape Algorithms

Force Directed Algorithms

wikipedia entry on force directed algorithms

Cytoscape mentions Jeff Heer.

Visualization Link by Jeff Heer

Fruchterman-Rheingold Algorithm

Spring Embedded Algorithms

Kamada and Kawai (1988).

JGraph Algorithms

JGraph Sourceforge link

jgraph web site

yWorks Algorithms

yWorks

yWorks algorithms are included in cytoscape, but they are proprietary. Here is an excerpt from the cytoscape documentation:

yFiles layouts are a set of commercial layouts which are provided courtesy of yWorks. Due to license restrictions,
the detailed parameters for these layouts are not available (there are no yFiles entries in the
Settings... dialog).

We do know this about the organic algorithm:

The organic layout algorithm is a kind of spring-embedded algorithm that combines elements of the other
algorithms to show the clustered structure of a graph.