CDAPS

Community Detection APplication and Service (CDAPS)

CDAPS performs multiscale community detection and functional enrichment for network analysis through a service-oriented architecture. These features are provided by integrating popular community detection algorithms and enrichment tools. All the algorithms and tools run remotely on a dedicated server.

Currently supported features:

  • Community detection algorithms: Louvain, Infomap, OSLOM, CliXO
  • Functional enrichment tools: g:Profiler, Enrichr, iQuery
_images/f1_app_store.png _images/f3.png

Feature Requests and Reporting Bugs

The CDAPS GitHub issue tracker can be used to report a bug or request a feature.

To Report a bug:

  • Go to https://github.com/cytoscape/cy-community-detection/issues
  • Click on New Issue
  • Write a short description of the issue. It is very helpful to provide a series of steps that can be taken to reproduce the issue.
  • If possible attach a session file (.cys) or example input files.
  • Enter App version, Cytoscape version and operating system.
  • Click on Submit new issue

Cite CDAPS

Manuscript in preparation

Installation

  • Cytoscape minimum version 3.7 is required.

Install Cytoscape

Download and install the latest version of Cytoscape at
http://www.cytoscape.org/download.php.

Install CyCommunityDetection

  • Open Cytoscape
  • In the main menu select Apps > App Manager
  • In the App Manager select CyCommunityDetection in the list of All Apps and click the Install button.
CyCommunityDetection can also be installed from the Cytoscape App Store at
http://apps.cytoscape.org/apps/cycommunitydetection

What’s New

Version 1.10.0

  • Added new menu option App -> Community Detection -> Settings that lets caller easily change CDAPS REST server. UD-1066
  • Added message letting user know using weight column in Community Detection dialog is an advanced parameter. UD-988
  • In Community Detection dialog replaced About button with info icon next to algorithm selection dropdown. UD-987

Bug fixes

  • Fixed bug where changes to properties under Edit -> Properties -> CyCommunityDetection were not being loaded. UD-986

Version 1.0

  • First release

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

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

Send terms in cluster to iQuery

Columns

This page describes the columns created by CDAPS in the network and node tables.

Network Columns

  • Columns created in network table when invoking Run Community Detection
_images/networkcolumns.png

  • name - String in format:

    Example:

  • __CD_OriginalNetwork - SUID of parent network. (Bug Saving/reloading a Cytoscape session changes SUID and will cause View Interactions for Selected Node to fail)

  • description - Contains string in this format:

    Example:

  • prov:wasDerivedFrom - Name of parent network

  • prov:wasGeneratedBy - Denotes version of CDAPS and algorithm used in this format:

    Example:

Node Columns

In the node table columns created by CDAPS are prefixed with CD_

  • Columns created in node table when invoking Run Community Detection
_images/cdetectnodecolumns.png
  • CD_MemberList - String of space delimited node names representing members of this cluster
  • CD_MemberList_Size - Size of CD_MemberList
  • CD_MemberList_LogSize - Log of CD_MemberList_Size
  • CD_CommunityName - Name of community set by invocation of Run Functional Enrichment
  • CD_AnnotatedMembers - String of space delimited node names used to set value in CD_CommunityName
  • CD_AnnotatedMembers_Size - Size of CD_AnnotatedMembers
  • CD_AnnotatedMembers_Overlap - CD_AnnotatedMembers_Size divided by CD_MemberList_Size
  • CD_AnnotatedMembers_Pvalue - Pvalue obtained from term mapping algorithm invoked by Run Functional Enrichment
  • CD_Labeled - Boolean denoting if CD_CommunityName was set to a value other then blank or (none)
  • Columns created in node table when invoking Run Functional Enrichment
_images/enrichnodecolumns.png

  • CD_AnnotatedAlgorithm - Algorithm used to set value in CD_CommunityName in format:

    Example:

  • CD_NonAnnotatedMembers - String of space delimited node names NOT used by algorithm to set mapped term in CD_CommunityName

  • CD_AnnotatedMembers_SourceDB Source database used by algorithm to set mapped term in CD_CommunityName

  • CD_AnnotatedMembers_SourceTerm Id of mapped term set in CD_CommunityName