Advanced Visualization: Node Position

This short protocol reviews how to use node position in Cytoscape.

Node Z Location

All nodes in Cytoscape have a Z Location property that defines its Z order on the canvas. Nodes with the same Z order are drawn at the same time, which can lead to important information being obscured. Z order can be set by the Z Location style property. Things to consider:

• Nodes with larger Z Location are drawn closer to the viewer (on top).
• Setting lots of different Z Location values can slow down graphics performance.
• The best approach is to use a few different Z Location values, or to set it manually using a bypass.

Controlling Node Z Location

For each property, styles are defined in columns Def. (default), Map. (mapping), and Byp. (bypass).

• Open the Yeast Perturbation example session from the Starter Panel.
• Go to the Style interface and then click the Properties drop-down at the top in the Node tab. This will show all available properties for Node.
• Select the Z Location to add it to the properties shown.
• To set a bypass for a selected node, for example STE12, click the Byp. column and enter a number. To move the node up, choose a value larger than the default.

In the below example, the selected node (yellow) has a Z Location value of 10, whereas the default value is 0.