cyTRON in an application for cancer progression analysis. It is an interface to the R library TRONCO and it supports both the visualization of already constructed models and the creation of new analysis.
cyTRON/JS was developed within the GSoC 2018 program, in collaboration with the NRNB organization.
During the program the following functionalities have been implemented:
- Graph visualization and manipulation: this was accomplished using Cytoscape.js and its extensions.
- Javascript-R communication: this was accomplished using the npm package
js-call-r. In particular it is possible to:- select input data in the formats suported by TRONCO (MAF, GISTIC and a custom boolean table)
- Select an input file with driver mutations
- Select a file with information about clusters into which the data needs to be splitted
- Reconstruct the model using TRONCO's algorithms
- Visualize the contructed model.
The web application was built using the Framework Express. The code is divided as follows:
- Controller: this is the folder where the functions to hadle the different HTTP requests are implemented. In particular it contains the R and JavaScript code necessary for the communication between cyTRON/JS and TRONCO.
- View: this is the folder which contains the interface.
- Routes: in this folder there is the code which maps each HTTP request to the corresponding function in the controller.
- Public: this is the folder which contains CSS and client-side JavaScript, which handles graph visualization.