CytoJSLayout is a Cytoscape layout plugin that supports Cytoscape.js layouts. The aim of the plugin is to enhance the layout capabilities of Cytoscape, an open-source software platform renowned for visualizing complex networks and integrating them with attribute data. While Cytoscape offers a plethora of automatic layout algorithms such as hierarchical, circular, force-directed, and CoSE (Compound Spring Embedder), it lacks support for certain advanced layouts available in its sister project, Cytoscape.js. These layouts, including fCoSE, CoLa, and CiSE, offer features and functionalities that are not present in the layouts currently supported by Cytoscape. Therefore, the plugin's focal point is to bridge this gap to include layouts supported by Cytoscape.js via SyBLaRS, a web-service suitable for this purpose. By incorporating these additional layouts, users can benefit from a broader range of options for organizing and visualizing networks, enabling more sophisticated analyses and insights into complex biological and computational systems.
The supported graph layout algorithms are:
- The plugin uses SyBLaRS service to process the network data to output the required layout.
- An active internet connection will be required for the plugin to communicate with the service.
- An alternative approach can be a locally hosted SyBLaRS service.
- TODO: Guide on how to change the SyBLaRS service url.
Clone the repository.
git clone https://github.com/tushar-c23/CytoLayoutChange to the cloned directory
mvn clean installManually
- Locate the compiled
target/CytoJSLayout-<version>.jarfile. - Copy the file to
CytoscapeConfiguration/3/apps/installedlocation. - Run
Cytoscape
via GUI
- Run
Cytoscape - Go to menu
Apps > App Store > Install apps from file - Select the
CytoJSLayout-<version>.jarfile
The plugin layouts will be available to be used in the layout menu.