MetNet Plugins for Cytoscape

Please read this tutorial to get started using Cytoscape.

The MetNet Plugins for Cytoscape (version 2.3 and above) are designed to help users explore complex networks by allowing the users to selectively explore the parts of a network that they are most interested in. The plug-ins are in three categories: data and subgraph manipulation, graph layouts and scripting.

Getting Started

NOTE: Before you install these plug-ins, you must install Cytoscape on your computer before use. After installing Cytoscape, please go through the MetNet getting started tutorial for details on loading networks and preferences. More tutorials for taking advantage of the base Cytoscape functionality can be found here.

Documentation

A pdf version of the user manual can be found here (out of date).

Installation

To use a plugin, download the jar file and put it in the Cytoscape "plugins" folder (the default location in Windows is C:\Program Files\Cytoscape-v2.x\plugins). The plugin should be automatically loaded the next time Cytoscape is started, and will appear as a menu item (in the plugins menu and/or when right-clicking a node).  Sample data for all plugins.

Plugin Description and Download

Data and Subgraph Manipulation

• Subgraph Creator
  • Purpose: Functions for flexible subgraph creation, node identification, cycle finder, and path finder in directed and undirected graphs. It also has a function to select the p-neighborhood of a selected node or group of nodes which can be selected by pathway name, node type, or by a list in a file. This generates a set of plug-ins called: path and cycle finding, p-neighborhoods and subgraph selection.
  • Cytoscape Version: 2.3 and above
  • Developers: Josette Etzel, Kyongryun Lee, Narasimha Rao Velagaleti
  • Last Updated: July 2008
  • Usage example and sample data for Subgraph creator
  • Documentation and sample data
• OmicsViz: Omics Data Translation and Viewing
  • Purpose: The OmicsViz plug-in provides translation capabilities between different sets of node names such as probe sets and gene loci or between probe sets of different species. For example, probe sets from grape or soybean may be mapped onto probe sets for Arabidopsis. This allows users to see how their genes of interest map onto the pathways for Arabidopsis and to view the expression values.
  • Cytoscape Version: 2.3 and above
  • Developer: Tian Xia
  • Last Updated: July 2008
  • Usage example and sample data for OmicsVis

Graph Layout

• Dot
  • Purpose: interfaces with the GraphViz package for graph layout. The plugin now supports both simple and rank-cluster layouts. This software uses the dot layout routine from the graphviz opensource software developed at AT&T labs.
  • Cytoscape Version: 2.3 and above
  • Developer: Paul Jennings and Kyongryun Lee
  • Last Updated: October 2007
  • Installation and Usage, sample data for Dot
    

Beta Plug-ins

These plugins have not been thoroughly tested yet, but they provide some useful functionality for linking R with Cytoscape. They have only been used on Linux.

• Animator
  • Purpose: The Animator plugin provides animation support to Cytoscape, so scripts running via Cytoscript may use animations to show results. Animations may affect anything controlled with the VizMapper tool, which includes color, shape, font face, arrow type, line type, size of font, node height and width, label and label color. Each frame of the animation consists of a Cytoscape VisualStyle object with an associated duration.
  • Cytoscape Version: 2.3 and above
  • Developer: Kyongryun Lee
  • Last Updated: September 2007
  • Usage example and sample animation script
• Animator-script
  • Purpose: The Animator-script plugin provides support for animations created in R. Animator-script is required to install CytoScript or any other plugins that run R in Cytoscape.
  • Cytoscape Version: 2.3 and above
  • Developer: Kyongryun Lee
  • Last Updated: September 2007
  • Usage example and sample animation script