I have been utilizing Cytoscape for a few days and find it very powerful. However, some its functionalities I am still trying to unlock. Here is a network I have graphed , but because of how dense it is - the edges are crossing over nodes they aren't connected to.
Is there any way this can be prevented? Here is an illustration of the problem I speak of.
Choose a different layout guaranteed to have no such overlaps, such as Attribute Circle, or tweak the force-directed layout parameters to make the gravitation parameter negative (to increase repulsion between nodes), and re-render.
You may also be interested in Hive plots, those are far more flexible than circular layout.
Another nice link is Mike Bostock's d3.js experiments with Krzywinski's hive plot technique: http://bost.ocks.org/mike/hive/
He includes a nice web demo that shows the effect of bundling links in categories, with adjustable parameters: http://mbostock.github.io/d3/talk/20111116/bundle.html
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I guess that is the only method then. Thank you.
Another method is to use hive plots, as Mikhail suggests.
As an example, I used them here to show qualitative, at-a-glance differences between classes of links separated by cell-specificity: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679407/figure/F2/
Drawing points on a circle is probably the "optimal" solution for keeping links in a network from overlapping, but even with a circular representation, I don't think there's an easy way to get around hairballs when you're dealing with large datasets, sorry.
Though I will note that a large set of networks can be compared at a glance, so that's a nice feature. Depends on what you're trying to communicate, I guess.