6. Nested Networks

Cytoscape has the ability to associate a Nested Network with any node. A nested network is any other network currently defined in Cytoscape. This capability allows for creation of network hierarchies as well as circular relationships. For example, various module-finding plugins make use of nested networks in the overview network that they generate. There each node representing a module contains a nested network.

6.1. Creating Nested Networks

There are currently two ways in which a user can create nested networks.

• By importing a Nested Network Format (NNF) file. (See: NNF Network Format).
• By manually constructing networks and assigning nested networks to individual nodes through the right-click node context menu. (See Nested Network Node Context Menu).

6.2. Visualization of Nested Networks

Nodes containing nested networks that are zoomed in sufficiently display an image for the nested network. If no current network view exists for the nested network the image will be a default icon, otherwise it will be a low-resolution rendering of the nested network’s current layout.