Diff for "Cytoscape_User_Manual/Nested_Networks"

Introducing Nested Networks

As of version 2.7, Cytoscape gained the ability to associate a nested network with a node. Such a nested network is not the network that the node is contained in but 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.

Creating Nested Networks

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

1. By importing a Nested Network Format (NNF) file. (See: ../Network_Formats#NNF).

2. By manually constructing networks and assigning nested networks to individual nodes through the right-click node context menu. (See: ../Navigation_Layout#Nested Network Node Context Submenu)

Visualisation 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.

Programmatically Manipulating Nested Networks

The giny.model.node interface defines two methods:

• public void setNestedNetwork(final GraphPerspective graphPerspective); This will assign a "network" (GraphPerspective) to a Node or replace the assigned network at a node if there was a prior existing one. In order to remove a nested network, please pass null to this method.

• public GraphPerspective getNestedNetwork(); If a Node has an associated nested network, it will be returned by this method. If no associated nested network exists, null will be returned instead.