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:

_images/starterpanel.png

If not displayed, the Starter Panel can be displayed by invoking the menu option View -> Show Starter Panel.

_images/loadstarterpanel.png

Run Community Detection

With the network loaded click on Apps -> Community Detection -> Run Community Detection menu option.

_images/runcommunitydetection.png

The above step will display a dialog seen below.

Select Louvain from algorithm dropdown and click Run button.

_images/communitydetectiondialog.png

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

_images/resultinghierarchy.png

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:

_images/term_map_select_nodes.png

The above step will display a dialog seen below:

Select gProfiler from algorithm dropdown and click Run button.

_images/term_map_dialog.png

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

_images/mapped_terms.png

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

_images/view_interactions_invoke.png

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

_images/view_interactions.png

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.

_images/runtallyattribs.png

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)

_images/runtallyattribsdialog.png

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

_images/resultingtallycols1.png

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:

_images/resultingtallypiechart.png

For more information click: Tally Attributes on Hierarchy