Many scientists use networks to visualize complex relationships among species, people, cities, genes, proteins or other subjects. Cytoscape is open-source software that is popular (6350 citations as of March 22nd 2016) for the visualization of networks. As scientists work with increasing amounts of data and the expectation of reproducible computational analyses increases, many users of network visualization programs are turning to scripted analyses instead of using a graphical user interface (GUI). Cytoscape has an application programming interface (API) that uses the Representational State Transfer (REST) to send information between Cytoscape and different programs. The package RCy3 allows users to connect R to Cytoscape allowing them to script their visualizations. There are two ways the package would be enhanced: 1) by enabling the use of Cytoscape plugins programmatically through their API, and 2) by creating robust walkthroughs of the code necessary to use RCy3 and other packages for reproducible network visualizations. The walkthroughs would include approaches relevant to many Cytoscape users and incorporate the programmatic use of plugins with developed function.




  • Augustin