(13D) Creation of a simplified network view

This creates a single group node for each cluster with a summarized name and provides an overview of the enrichment result themes that is useful for enrichment maps containing many nodes.

Collapse Network

  1. In the Control Panel, select the AutoAnnotate tab.
  2. Click on the Menu icon in the upper right corner.
  3. Select Collapse All.

node slider

Pop-up after selecting Collapse all shows up every time user collapses the clusters

Once you click on Collapse All, a pop-up window will show the message ‘Before collapsing clusters please go to the menu Edit → Preferences → Group preferences and select ‘Enable attribute aggregation’’.

node slider

  • There is no need to adjust this parameter repeatedly.
  • Click on Don’t ask me again and OK if you have set this parameter previously.

Collapsing the network takes a long time

For large networks, collapsing and expanding may take time. For a quick view of the collapsed network, you can create a summary network by selecting the Create summary Network… option. There are two options for the summary network: clusters only, which creates a summary network with just the circled clusters, or clusters and unclustered nodes, which creates a summary network that also includes the singleton nodes that are not part of any cluster

Collapsed network contains gray nodes instead of colored nodes as they were in the pre-collapsed network

If the nodes in the resulting collapsed network are gray, then you forgot to enable attribute aggregation.

  • Expand the clusters and,
  • before collapsing clusters again, go to Edit → Preferences → Group preferences and
  • select Enable attribute aggregation
  • Now, Select Collapse all to collapse network.

node slider

The enrichment map was summarized by collapsing node clusters using the AutoAnnotate application. Each cluster of nodes s now represented as a single node.

Scale Network

Scale the collapsed network for better viewing.

  1. In the Cytoscape menu bar, select View → Show Tool Panel.
  2. Go to the Layout Tools panel located at the bottom of the Control Panel.
  3. Locate the Scale slider bar and use it on unselected nodes (uncheck Selected only).
  4. Move the slider left to tighten the node spacing. Close the Node Layout Tools panel when finished.

node slider