Interactive visualization and manipulation of nested networks

[Up] [Top]

Documentation for package ‘RedeR’ version 1.26.0

Help Pages

A C D E G H I M N P R S U V

RedeR-package RedeR: bridging the gap between network analysis and visualization.

-- A --

addEdgeBetweenContainers Add edges between containers.
addEdgeBetweenContainers-method Add edges between containers.
addEdges Add edges to RedeR graphs.
addEdges-method Add edges to RedeR graphs.
addGraph Add graphs to RedeR application.
addGraph-method Add graphs to RedeR application.
addLegend.color Add graph legends to RedeR application.
addLegend.color-method Add graph legends to RedeR application.
addLegend.shape Add graph legends to RedeR application.
addLegend.shape-method Add graph legends to RedeR application.
addLegend.size Add graph legends to RedeR application.
addLegend.size-method Add graph legends to RedeR application.
addNodes Add nodes to RedeR graphs.
addNodes-method Add nodes to RedeR graphs.
addSeries Add series to RedeR application.
addSeries-method Add series to RedeR application.
addSubgraph Add subgraphs to RedeR application.
addSubgraph-method Add subgraphs to RedeR application.
addSubgraph.list Add a list of subgraphs to RedeR application.
addSubgraph.list-method Add a list of subgraphs to RedeR application.
att.mape Map and set edge and vertex attributes to RedeR application.
att.mapv Map and set edge and vertex attributes to RedeR application.
att.sete Map and set edge and vertex attributes to RedeR application.
att.setv Map and set edge and vertex attributes to RedeR application.

-- C --

calld Call RedeR app from R.
calld-method Call RedeR app from R.
Carroll2006 Pre-processed dataset for RedeR case study.
cea Co-expression analysis.

-- D --

deleteEdges Remove edges from RedeR graphs.
deleteEdges-method Remove edges from RedeR graphs.
deleteNodes Remove nodes from RedeR graphs.
deleteNodes-method Remove nodes from RedeR graphs.
deleteSelectedEdges Delete selected edges in RedeR graphs.
deleteSelectedEdges-method Delete selected edges in RedeR graphs.
deleteSelectedNodes Delete selected nodes in RedeR graphs.
deleteSelectedNodes-method Delete selected nodes in RedeR graphs.
deSelectEdges Unmark selected edges.
deSelectEdges-method Unmark selected edges.
deSelectGraph Unmark selected graph objects.
deSelectGraph-method Unmark selected graph objects.
deSelectNodes Unmark selected nodes.
deSelectNodes-method Unmark selected nodes.
duplicateGraph Duplicate graphs in RedeR application.
duplicateGraph-method Duplicate graphs in RedeR application.

-- E --

ER.deg Pre-processed dataset for RedeR case study.
ER.limma Pre-processed dataset for RedeR case study.
exitd Exit RedeR R-to-Java interface.
exitd-method Exit RedeR R-to-Java interface.

-- G --

getContainerComponets Get container components.
getContainerComponets-method Get container components.
getEdgeIDs Get edge IDs.
getEdgeIDs-method Get edge IDs.
getEdges Get edges.
getEdges-method Get edges.
getGraph Get RedeR graph.
getGraph-method Get RedeR graph.
getNodeIDs Get node IDs.
getNodeIDs-method Get node IDs.
getNodes Get nodes.
getNodes-method Get nodes.
getSourceEdgeIDs Get source-edge IDs.
getSourceEdgeIDs-method Get source-edge IDs.
getTargetEdgeIDs Get target-edge IDs.
getTargetEdgeIDs-method Get target-edge IDs.
gtoy.rm Random graphs and modules.

-- H --

hs.inter Pre-processed dataset for RedeR case study.

-- I --

isDynamicsActive Inquires about RedeR current state.
isDynamicsActive-method Inquires about RedeR current state.

-- M --

mergeNodes Merge nodes.
mergeNodes-method Merge nodes.
mergeOutEdges Merge out-edges between connected containers and transfers edges from nodes to containers.
mergeOutEdges-method Merge out-edges between connected containers and transfers edges from nodes to containers.

-- N --

nesthc Nest hclust objects to containers.
nesthc-method Nest hclust objects to containers.
nestNodes Nest nodes to containers.
nestNodes-method Nest nodes to containers.

-- P --

ping Test RedeR R-to-Java interface.
ping-method Test RedeR R-to-Java interface.

-- R --

RedeR RedeR: bridging the gap between network analysis and visualization.
RedPort The constructor for the RedPort class.
RedPort-class Class "RedPort"
relax relax
relax-method relax
resetd Reset RedeR app.
resetd-method Reset RedeR app.

-- S --

selectAllEdges Select all edges.
selectAllEdges-method Select all edges.
selectAllNodes selectAllNodes
selectAllNodes-method selectAllNodes
selectEdges selectEdges
selectEdges-method selectEdges
selectGraph Select graph.
selectGraph-method Select graph.
selectNodes Select nodes.
selectNodes-method Select nodes.
setArrowDirection Set arrow direction.
setArrowDirection-method Set arrow direction.
subg Subgraph of a graph.

-- U --

updateContainerSize Update container size.
updateContainerSize-method Update container size.
updateGraph Update RedeR graphs.
updateGraph-method Update RedeR graphs.

-- V --

version Version
version-method Version