Is anybody aware of a possibility (e.g. probably a plugin) to use Cytoscape for representing protein interaction networks in a kind of 'cellular layout' ?
Several pieces of commercial software are offering this option, e.g. by drawing a cell schematic (with nucleus, cytoplasm, plasma membrane, and maybe a few organelles) and then running a layout algorithm where each protein with known localization has to stay within the space reserved for this compartment. Unfortunately, I have not seen any similar for Cytoscape.
For what I currently have in mind, it would be sufficient to define a few boxes on the canvas (by ID and coordinates) and then provide a node attribute that defines where on the canvas the node is allowed to sit. It should then be possible to run a standard layout (e.g. spring-embedded) using the boxes as boundary conditions.
I imagine that I am not the only one who has this idea and that somebody might have tried this before.