Best way to make a graph edges shorter/ network more compact

[HizJ]

Hi 

I am attempting to use automation to plot a network, and prefer to use the perfuse force directed layout but I find that the edge lengths are too long and the network is very scattered.

I know I can change the position of nodes by dragging them on the display, or by changing the parameters of the layout.

I was wondering is there some other way using automation to ensure that the edge lengths are as short as possible, or someway to compact the network ? 

[Alex Pico]

Certainly. All Cytoscape-provided layouts are tunable, including Prefuse Force Directed. And tunables are supported by automation. Open up the Layout > Settings dialog to become familiar with the parameters you can tune (See video: https://www.youtube.com/watch?v=YPdbjIDD9vA).  Then open the Automation Panel (View menu) to test out your scripting syntax, e.g.,   

help layout force-directed # will display names for all parameters

layout force-directed defaultSpringLength=30. # will perform the layout with a shorter default edge length

Finally, if you are running your scripts in R, you can use the RCy3 function, like so:

layoutNetwork('force-directed defaultSpringCoefficient=0.0000005’). # will perform the layout with looser springs

Include as many tunable parameters as you like, space separated.

Hope this helps!

 - Alex

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