# Interactive visualization and manipulation of nested networks

## Documentation for package ‘RedeR’ version 3.4.0

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

## Help Pages

addEdgeBetweenContainers | Deprecated functions
addEdges | addEdges
addEdges-method | addEdges
addGraph | Adding 'igraph' objects to RedeR
addGraph-method | Adding 'igraph' objects to RedeR
addGraphToRedeR | Adding 'igraph' objects to RedeR
addLegend.color | Deprecated functions
addLegend.shape | Deprecated functions
addLegend.size | Deprecated functions
addLegendToRedeR | Adding graph legends to the RedeR app
addNodes | addNodes
addNodes-method | addNodes
att.adde | Transforming edge and vertex attributes
att.addv | Transforming edge and vertex attributes
att.mape | Deprecated functions
att.mapv | Transforming edge and vertex attributes
att.sete | Transforming edge and vertex attributes
att.setv | Transforming edge and vertex attributes
calld | Call RedeR app from R
calld-method | Call RedeR app from R
cea | Deprecated functions
deleteEdges | deleteEdges
deleteEdges-method | deleteEdges
deleteNodes | deleteNodes
deleteNodes-method | deleteNodes
deleteSelectedEdges | Deprecated functions
deleteSelectedNodes | Deprecated functions
Deprecated | Deprecated functions
deSelectEdges | Deprecated functions
deSelectGraph | Deprecated functions
deSelectNodes | Deprecated functions
ER.limma | Pre-processed dataset for RedeR case studies.
exitd | Exit the RedeR R-to-Java interface
exitd-method | Exit the RedeR R-to-Java interface
exitRedeR | Exit the RedeR R-to-Java interface
getContainerComponets | Deprecated functions
getEdgeIDs | Deprecated functions
getEdges | Deprecated functions
getGraph | Get graphs from RedeR
getGraph-method | Get graphs from RedeR
getGraphFromRedeR | Get graphs from RedeR
getNodeIDs | Deprecated functions
getNodes | Deprecated functions
getSourceEdgeIDs | Deprecated functions
getTargetEdgeIDs | Deprecated functions
gtoy.rm | Deprecated functions
hs.inter | Pre-processed igraph object for RedeR case studies.
mergeNodes | Deprecated functions
mergeOutEdges | mergeOutEdges
mergeOutEdges-method | mergeOutEdges
nesthc | Deprecated functions
nestNodes | nestNodes
nestNodes-method | nestNodes
ping | Ping RedeR app
ping-method | Ping RedeR app
pingRedeR | Ping RedeR app
RedeR-data1 | Pre-processed igraph object for RedeR case studies.
RedeR-data2 | Pre-processed dataset for RedeR case studies.
RedPort | Constructor of RedPort-class objects
RedPort-class | RedPort: An S4 class for RedeR graphics
relax | Relax
relax-method | Relax
relaxRedeR | Relax
resetd | Reset RedeR app
resetd-method | Reset RedeR app
resetRedeR | Reset RedeR app
selectAllEdges | Deprecated functions
selectAllNodes | Deprecated functions
selectEdges | selectEdges
selectEdges-method | selectEdges
selectGraph | Deprecated functions
selectNodes | selectNodes
selectNodes-method | selectNodes
setArrowDirection | Deprecated functions
startRedeR | Start RedeR app from R
subg | Subgraph of a graph
transform.attributes | Transforming edge and vertex attributes
updateContainerSize | Deprecated functions
updateCoordXY | Deprecated functions
updateGraph | Deprecated functions
updateLayoutFromRedeR | Update graph layout
version | Version
version-method | Version