Dot Plugin: Installation and Usage Example

dot.jar interface to 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: August 2007

Installation Instructions for the Dot Plugin

1. Download the dot.jar file and put it in the Cytoscape Plugin directory.
2. Download and install the appropriate Graphviz package for your operating system from www.graphviz.org. This plugin has been verified for Graphviz versions 2.12-2.14. Specific platform notes are given below:
   • Linux users have the option of either installing the entire GraphViz package or downloading the Linux dot executable and putting it in the Cytoscape plug-in folder.
   • Mac: The Mac installers are located under the heading "Third-Party (non-AT&T) Executable Packages" on the download page.
3. Open Cytoscape and set the path to the dot application. Before using the dot plugin for the first time, go to the menu item Layout and select the “Configure dot layout” option.
   
   The window below will come up.
   
4. Set the path to the dot.exe application which should be in the following locations:
   • Windows: c:\Program Files\ATT\Graphviz\bin\dot.exe
   • Mac - /opt/graphviz/bin/dot
   • Linux – Either /usr/bin/dot or /usr/local/bin/dot
5. Usage example and sample data

Page last updated 31 October 2007