Columns.rst

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

• name - String in format:

  <ALGORITHM NAME>_(<WEIGHT COLUMN USED OR no column used>)_<NAME OF PARENT NETWORK>
  

  Example:

  infomap_(none)_HIV_human PPI
  

• __CD_OriginalNetwork - SUID of parent network. This value can change upon session save/reload. If CDAPS is unable to find the parent network a dialog will be displayed to the user letting them select the correct parent network.

  Note

  Setting the value of __CD_OriginalNetwork network attribute to a negative value will display the Parent network dialog chooser the next time :ref:`View Interactions <view-interactions>` is invoked

• description - Contains string in this format:

  Original network: <NAME OF PARENT NETWORK>
  Algorithm used for community detection: <INTERNAL NAME OF COMMUNITY DETECTION ALGORITHM>
  Edge table column used as weight: <WEIGHT COLUMN USED OR (none)>
  CustomParameters: {<CUSTOM PARAMETERS SET BY CALLER>}
  

  Example:

  Original network: HIV-human PPI
  Algorithm used for community detection: infomap
  Edge table column used as weight: (none)
  CustomParameters: {--markovtime=0.75}
  

• prov:wasDerivedFrom - Name of parent network

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

  App: CyCommunityDetection (<VERSION>) Docker Image: <DOCKER IMAGE USED>
  

  Example:

  App: CyCommunityDetection (1.1) Docker Image: coleslawndex/cdinfomap:0.1.0
  

Node Columns

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

• Columns created in node table when invoking Run Community Detection

• 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

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

  Annotated by <ALGORITHM NAME> [Docker: <DOCKER IMAGE>] {<CUSTOM PARAMETERS>} via CyCommunityDetection Cytoscape App (<VERSION>)
  

  Example:

  Annotated by gProfiler [Docker: coleslawndex/cdgprofilergenestoterm:0.3.0] {{--maxpval=0.00001, --minoverlap=0.05, --maxgenelistsize=5000}} via CyCommunityDetection Cytoscape App (1.1)
  

• 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

• Columns created in node table when invoking Tally Attributes on Hierarchy

• CommunityDetectionTally::<TALLY SELECTED COLUMNS> - Each column selected in the tally will have an entry and the value is the count of members that did have a positive or true value in the column on the parent network
• CommunityDetectionTally::Unmatched - Count of members in hierarchy cluster node that did NOT have a positive or true value in any of the tally columns

Note

CommunityDetectionTally is the namespace prefixed onto columns created when invoking Tally Attributes on Hierarchy

For more information click: :ref:`Tally Attributes on Hierarchy <tally-attributes-on-hierarchy>`