- Go to the Cytoscape menu and select: Plugins → Random Network Plugin → Randomize Existing Network
- The below dialog will open:
- Edge Shuffle: This checkbox is redundant, it will be removed unless other randomization techniques are added. Currently there is only one way to randomize a network.
- Number of networks to create: This option allows the user to specify how many networks should be created at once. The value must be an integer greater than 1.
- Num Shuffles: The number of shuffles that will be performed. This number is automatically set to the number of edges in the currently selected network. This number must be an integer greater than 1. As this number increases, the resulting network will become more randomized.
- Treate as Undirected?: If this checkbox is selected then the resulting Cytoscape network may only have a single edge between any two nodes. As of Cytoscape 2.6.0 only directed edge may actually exist, however, this should change as of v.3.0.
- Below is the resulting network from the values given above.
galFiltered network with organic layout (331 nodes, 362 edges)
Randomized version of galFiltered (331 nodes, 362 edges).
Node positions are the same as in the un-randomized version, however, the edges have been shuffled resulting in longer edge lengths.
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