Interactive visualization and manipulation of nested networks.

Documentation for package ‘RedeR’ version 1.6.1

DESCRIPTION file.
Overview of user guides and package vignettes; browse directory.
Package NEWS.

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.
deletePlugin	Remove plugins from RedeR application.
deletePlugin-method	Remove plugins from RedeR application.
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.
dynwin	Wrap R graphics.
dynwin-method	Wrap R graphics.

-- 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 --

getArrowDirection	Get arrow direction.
getArrowDirection-method	Get arrow direction.
getContainerComponets	Get container components.
getContainerComponets-method	Get container components.
getEdgeColor	Get edge color.
getEdgeColor-method	Get edge color.
getEdgeIDs	Get edge IDs.
getEdgeIDs-method	Get edge IDs.
getEdges	Get edges.
getEdges-method	Get edges.
getEdgeType	Get edge type.
getEdgeType-method	Get edge type.
getEdgeWeight	Get edge weight.
getEdgeWeight-method	Get edge weight.
getEdgeWidth	Get edge width.
getEdgeWidth-method	Get edge width.
getGraph	Get RedeR graph.
getGraph-method	Get RedeR graph.
getNodeAliases	Get node aliases.
getNodeAliases-method	Get node aliases.
getNodeBend	Get node bend.
getNodeBend-method	Get node bend.
getNodeColor	Get node color.
getNodeColor-method	Get node color.
getNodeFontColor	Get font color.
getNodeFontColor-method	Get font color.
getNodeFontName	Get font name.
getNodeFontName-method	Get font name.
getNodeFontSize	Get font size.
getNodeFontSize-method	Get font size.
getNodeFontStyle	Get font style.
getNodeFontStyle-method	Get font style.
getNodeFontX	Get font x coordinate.
getNodeFontX-method	Get font x coordinate.
getNodeFontY	Get font y coordinate.
getNodeFontY-method	Get font y coordinate.
getNodeH	Get node height.
getNodeH-method	Get node height.
getNodeIDs	Get node IDs.
getNodeIDs-method	Get node IDs.
getNodeLineColor	Get node-line color.
getNodeLineColor-method	Get node-line color.
getNodeLineWidth	Get node-line width.
getNodeLineWidth-method	Get node-line width.
getNodes	Get nodes.
getNodes-method	Get nodes.
getNodeShape	Get node shape.
getNodeShape-method	Get node shape.
getNodeSize	Get node size.
getNodeSize-method	Get node size.
getNodeW	Get node with.
getNodeW-method	Get node with.
getNodeWeight	Get node weight.
getNodeWeight-method	Get node weight.
getNodeX	Get node x coordinate.
getNodeX-method	Get node x coordinate.
getNodeY	Get node y coordinate.
getNodeY-method	Get node y coordinate.
getSourceEdgeIDs	Get source-edge IDs.
getSourceEdgeIDs-method	Get source-edge IDs.
getSourceEdges	Get source edges.
getSourceEdges-method	Get source edges.
getTargetEdgeIDs	Get target-edge IDs.
getTargetEdgeIDs-method	Get target-edge IDs.
getTargetEdges	getTargetEdges
getTargetEdges-method	getTargetEdges
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.
PluginBuilder	The constructor for the PluginBuilder class.
PluginBuilder-class	Class 'PluginBuilder'
pluginParser	RedeR plugin parser.

-- R --

RedeR	RedeR: bridging the gap between network analysis and visualization.
rederexpresspost	Remote procedure calls optimized for RedeR.
rederpost	Remote procedure calls optimized for RedeR.
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.
setEdgeColor	Set edge color.
setEdgeColor-method	Set edge color.
setEdgeType	Set edge type.
setEdgeType-method	Set edge type.
setEdgeWeight	Set edge weight.
setEdgeWeight-method	Set edge weight.
setEdgeWidth	Set edge width.
setEdgeWidth-method	Set edge width.
setNodeAlias	Set node alias.
setNodeAlias-method	Set node alias.
setNodeBend	Set node bend.
setNodeBend-method	Set node bend.
setNodeColor	Set node color.
setNodeColor-method	Set node color.
setNodeFontColor	Set font color.
setNodeFontColor-method	Set font color.
setNodeFontName	Set font name.
setNodeFontName-method	Set font name.
setNodeFontSize	Set font size.
setNodeFontSize-method	Set font size.
setNodeFontStyle	Set font style.
setNodeFontStyle-method	Set font style.
setNodeFontXY	Set font x,y coordinates.
setNodeFontXY-method	Set font x,y coordinates.
setNodeLineColor	Set node-line color.
setNodeLineColor-method	Set node-line color.
setNodeLineWidth	Set node-line width.
setNodeLineWidth-method	Set node-line width.
setNodeShape	Set node shape.
setNodeShape-method	Set node shape.
setNodeSize	Set node size.
setNodeSize-method	Set node size.
setNodeWeight	Set node weight.
setNodeWeight-method	Set node weight.
setNodeXY	Set node x,y coordinates.
setNodeXY-method	Set node x,y coordinates.
subg	Subgraph of a graph.
submitPlugin	Submit plugins to RedeR application.
submitPlugin-method	Submit plugins to RedeR application.

-- U --

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

-- V --

version	Version
version-method	Version