Is it possible to show a neighborhood analysis with relative distances by defined scores in cytoscape? As an example: 2=not in the direct neighborhood, 1=in the direct neighborhood, 0=random permutation.
To take larger values is a very good and I will also implement this in my analysis. Unfortunately, I'm still unclear which method I should use for the visualization of the relative distances. According to what I had read the "force-directed" paradigm should be the best solution for my analysis. Do someone agree with that? Thanks in advance and best regards Joschua
Sure, you could certainly do something like that. The real question is what would you want the network to look like? If you are trying to see some sort of clustering effect by using your relative distances, I would use different numbers -- maybe 100=not in the direct neighborhood, 1=in the direct neighborhood, and blank for random permutations. If you want to use your relative distances for something else (e.g. edge type or color), then the scaling shouldn't matter.