Finding Clusters with AutoAnnotate

The AutoAnnotate app must be installed for this functionality. https://apps.cytoscape.org/apps/autoannotate

At the bottom of the main EnrichmentMap panel there is a button that says Find Clusters.

This button provides two options:

• Use AutoAnnotate to find clusters of similar nodes

  • This option simply opens the AutoAnnotate dialog. For more information on all the options for finding and highlighting clusters see the AutoAnnotate docs: https://autoannotate.readthedocs.io/en/latest/CreatingAnAnnotationSet.html

• Highlight significant nodes

  • This option runs AutoAnnotate automatically. It finds clusters of highly significant nodes and simply highlights the most significant node in each cluster. Highlighted nodes are given larger labels.

  • The clusters can be seen in the AutoAnnotate main panel. https://autoannotate.readthedocs.io/en/latest/WorkingWithAutoAnnotate.html

Significance

The attribute used to determine significance is based on the current Chart Data setting in the Style panel. If you change the Chart Data attribute it will update the highlighted nodes accordingly.