Interactive visualization and manipulation of nested networks

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Documentation for package ‘RedeR’ version 1.40.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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

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.adde	Add, map, and set edge and vertex attributes to the RedeR application.
att.addv	Add, map, and set edge and vertex attributes to the RedeR application.
att.mape	Add, map, and set edge and vertex attributes to the RedeR application.
att.mapv	Add, map, and set edge and vertex attributes to the RedeR application.
att.sete	Add, map, and set edge and vertex attributes to the RedeR application.
att.setv	Add, map, and set edge and vertex attributes to the 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

-- misc --

.rederpost	This function implements an RPC protocol for RedeR.
.rederpost-method	This function implements an RPC protocol for RedeR.