I am trying to find a web-based tool to visualize protein interaction networks. I want to visualize large networks, so interactivity would be an impossible task, but I would like to offer the possibility of clicking on a node to see the details of the protein. Furthermore, the protein interactions to be visualized, would be predicted from a machine learning technique, so there would be a confidence score for each protein interaction. I would like to embed this score in the (width of the) edges of the network.
I have looked through many visualization tools, like Cytoscape, which is based on Flash (not suitable for large network visualization), and Gephi combined with Seadragon, (the first is a standalone application for network visualization, while the second helps somebody deploy the network on the web), but the process of exporting the net has to be made manually. I haven't found a visualization tool that can satisfy the requirements I mentioned above.
I would like to ask if there is a web-based network visualization tool, which is suitable for visualizing large weighted networks, with minimum interaction (clicking on nodes).
1 answer
You could try BioLayout.
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Perhaps you could build one with d3.js and an HTML5 canvas. The d3 component gives you a quick network layout engine, while the canvas portion can be used to gain speed and render larger-scale networks.
Here is a tutorial for that:http://flowingdata.com/2012/08/02/how-to-make-an-interactive-network-visualization/