java,graph-visualization,prefuse
One approach might be to add a JForcePanel, which is a Swing component for configuring the parameters of the Force functions in a given ForceSimulator. Useful for exploring different parameterizations when crafting a visualization. This might help you to find the optimal parameters to use in your implementation of getForceSimulator()....
You add a color action for VisualItem.STROKECOLOR and give it the edge-group as a key, possibly with a predicate if you want to assign that colour only to certain edges new ColorAction(GROUP_EDGES, (myPredicate, ) VisualItem.STROKECOLOR, myColor) ...