Using an External Clustering Algorithm

AutoAnnotate allows clusters to be defined using any node attribute via the User-defined clusters option on the Advanced panel. This allows clustering algorithms provided by other Cytoscape Apps or by external scripts to be used with AutoAnnotate.

Using clusterMaker Manually

You may use some clusterMaker algorithms not provided through the New Annotation Set dialog.

Here is an example using the clusterMaker Transitivity Clustering algorithm.

  • Select Apps > clusterMaker Cluster Network > Transitivity Clustering.
  • A dialog with algorithm settings will be shown.
  • Expand the Cytoscape Advanced Settings section and take note of the Cluster Attribute Name, in this case it is __transclustCluster.
  • Click Ok to run the algorithm.
  • A node attribute (column) called __transclustCluster is created where each node is assigned a cluster identifier.
  • Open the New Annotation Set dialog and choose the Advanced panel.
  • Select User-defined clusters and then select the __transclustCluster column.
  • Click Create Annotations.

AutoAnnotate does not support overlapping clusters. Some clusterMaker algorithms create list columns that may assign some nodes to more than one cluster. These columns cannot be used with AutoAnnotate.

Using the MCODE App

The MCODE App is a popular clustering App that works well with AutoAnnotate.

Using MCODE with AutoAnnotate

  • Select Apps > MCODE
  • A dialog with algorithm settings will be shown.
    • If the dialog does not appear, then go to the MCODE panel and click the (+) icon at the top of the panel.
  • In the MCODE dialog click the Analyze Current Network button.
  • Open the New Annotation Set dialog and choose the Advanced panel.
  • Select User-defined clusters and then select the MCODE Clusters (1) column.
  • Click Create Annotations.

Using External Scripts

See the Automating AutoAnnotate for details on how to automate Cytoscape using external scripts.

A script must do the following to provide clusters to AutoAnnotate:

  • Create a node attribute (column), any type may be used.
  • Use the node attribute to assign a cluster identifier to each node. The cluster identifier may be blank, those nodes will not be included in clusters.
  • Open the New Annotation Set dialog and choose the Advanced panel.
  • Select User-defined clusters and then select the __mcodeCluster column.
  • Click Create Annotations.