# Interactive visualization and manipulation of nested networks

## Documentation for package ‘RedeR’ version 2.4.0

- 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 | Display 'igraph' objects in the RedeR application.
addGraph-method | Display 'igraph' objects in the 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 --

isRelaxActive | Inquires about RedeR current state.
isRelaxActive-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.
updateCoordXY | Update node coordinates.
updateCoordXY-method | Update node coordinates.
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.