Quick Tutorial¶
Open a network¶
To run Community Detection, a network must be loaded in Cytoscape.
From within Cytoscape click on Affinity Purification network on the starter panel:

If not displayed, the Starter Panel can be displayed by invoking the menu option View -> Show Starter Panel.
Run Community Detection¶
With the network loaded click on Apps -> Community Detection -> Run Community Detection menu option.

The above step will display a dialog seen below.
Select Louvain from algorithm dropdown and click Run button.

A new network/hierarchy should be generated as seen here (The current default layout will be used):

Note
Each node in the network/hierarchy above represents a cluster with the members of that cluster set in the CD_MemberList node column
Perform Term Mapping¶
Using network/hierarchy generated above select a few nodes in the network view and then right click on a selected node to display the submenu and select Apps -> Community Detection -> Run Functional Enrichment as seen here:

The above step will display a dialog seen below:
Select gProfiler from algorithm dropdown and click Run button.

gProfiler will be run and nodes will be named and colored according to overlap as seen here:

View Interactions¶
Using network/hierarchy generated above select a single node in the network view and then right click on the selected node to display the submenu and select Apps -> Community Detection -> View Interactions for Selected Node

Invoking this menu option will show all the nodes pertaining to this cluster in the parent network like as seen here:

Tally Attributes on Hierarchy¶
With a CDAPS hierarchy network (as generated via Run Community Detection step above) click on Apps -> Community Detection -> Tally Attributes on Hierarchy menu option.

The above step will display a dialog seen below.
Select one or more columns from parent network to tally on hierarchy network and click OK button. (only columns of type Integer, Boolean, or Double will be listed)

New corresponding columns will be added to the hierarchy network node table as seen below.

These new columns match the names of the columns selected in the dialog, but with the namespace CommunityDetectionTally prefixed.
In addition, a CommunityDetectionTally::Unmatched column will also be added.
Note
These columns can be used to create charts on each node as described here
Example hierarchy network styled with node charts:

For more information click: Tally Attributes on Hierarchy