Bridging the gap between hierarchical network representation and functional analysis.


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Documentation for package ‘RedeR’ version 1.2.5

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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