Advanced Visualization: Adjusting the View

This short protocol reviews how to adjust the network view in Cytoscape.

Adjusting the View

Node layout tools provide important tools to help adjust the final look of a network, and are available under Layout→Node Layout Tools. The tools include:

  • Scaling of width, height for all or selected nodes.
  • Align nodes
  • Distribute nodes
  • Stack nodes
  • Rotate all or selected nodes

Rotate Nodes

For example, we can select a part of the network and rotate it.

  • Open the Yeast Perturbation example session from the Starter Panel.
  • Select a set of nodes in the network.
  • In the Layout Tools, check the Selected Only checkbox in the Rotate section.
  • Move the degree slider to 90.

Notice that the selected nodes are rotated 90 degrees.

Scale Nodes

Similarly, we can scale a set of nodes in a network.

  • With the same set of nodes selected, check the Selected Only checkbox in the Scale section.
  • Move the degree slider to the left, about 1/4 point.

Notice that the selected nodes are now scaled closer to each other.