# Bridging the gap between hierarchical network representation and functional analysis.

## Documentation for package ‘RedeR’ version 1.0.14

- 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