Advanced Visualization: Tuning Layouts

This short protocol reviews how to tune layout algorithms in Cytoscape.

Tuning Layouts

In general, most layouts can be tuned to improve the aesthetics. Recommended approach:

Go to Layout→Settings. Select a layout of choice, for example Prefuse Force Directed and click Apply Layout. This will apply the layout with the default settings.
Next, change a parameter, for example Default Spring Coefficient or Default Spring Length, and apply the layout again.
Observe the results. If you get the result you want, click Done, otherwise click Edit→Undo and apply the layout again.

Example: Prefuse Force Directed Layout

The below images shows the difference in the Yeast Perturbation network from decreasing the Spring Coefficient for the Prefuse Force Directed Layout by a factor of 10.

Prefuse force-directed layout with default settings.

Prefuse force-directed layout with a decreased Spring Coefficient .