Advanced Visualization: Style Properties

This short protocol reviews advanced style options available.

Viewing and Adding Properties

Cytoscape has many style properties that are not shown by default.

• Go to the Style interface and then click the Properties drop-down at the top. This will show all available properties for either Node, Edge or Network.
• Properties with a checkmark are those currently displayed in the Style interface. To add a property in order to use it for visualization, simply select the property in the list.

Mapping, Default and Bypass

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

• Without a specific style mapping, each property will be defined by its Default.
• Any mappings defined by the user or current style will be shown in the Mapping column.
• Bypass is used to override both the mapping (if any) and the default.

Setting a Bypass

The following example uses the Yeast Perturbation example session file.

• Select the nodes or edges in the network for which you want to set the visual property. In the example below, the STE12 node is selected.
• In the Style panel for Node, click the Map. column for Fill Color. Note the existing mapping to gal1RGExp.
• Click the Byp. column, and in the interface that opens, set the value as desired, for example red.

Setting a Bypass

The resulting style will look like this:

• The altered properties will be permanently set for the selected nodes or edges.
• To clear the value, select the nodes or edges again, right-click on the Byp.column and select Remove Bypass.