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):
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:
