Cytoscape NetLink Plugin

The NetLink plugin is a simple Cytoscape plugin for connecting nodes or edges in one network with another network. The basic idea is to use an attribute which points to a network name which is in turned used for linking nodes and edges to other networks.

The NetLink plugin simply looks for an attribute named netlink.connection and if that attribute exists for the given node or edge, it then creates a menu item in the right-click (context) popup menu. If the menu item exists, then chosing the menu item will switch the selected network view focus from the current network to the new network.

Download + Install

You can install the NetLink plugin automatically from the PluginManager found in the Plugin -> Manage Plugins menu within Cytoscape.

Alternatively, you can download the plugin manually from the Cytoscape Plugins Page, copy the NetLink.jar file to your plugins directory, and restart Cytoscape.

Example: Parent -> Child Links

Begin with a simple network called Parent.sif:

A pp B
B pp C
C pp A

Next, assume that node A points to child network A.sif, B points to child network B.sif, and C points to child network C.sif.


one pp two
two pp three


marge knows homer
lisa knows bart


cat xx dog
bird xx fish

Now, to create the links from the Parent nodes to the child nodes, create a node attribute file where the attribute is named netlink.connnection.

A = A.sif
A = B.sif
A = C.sif

Now load all networks and the node attributes file. When you right click on a node in the Parent.sif network, you should see a menu item that says: "asdf".

Example: Child -> Parent Links

If you want to add Child ->Parent links, then simply append the node names found in the child networks the node attributes file that you just created:

A = A.sif
B = B.sif
C = C.sif
one = Parent.sif
two = Parent.sif
three = Parent.sif
cat = Parent.sif
dog = Parent.sif