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RedeR (version 1.20.0)

Interactive visualization and manipulation of nested networks

Description

RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of modular structures, nested networks and multiple levels of hierarchical associations.

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Version

Version

1.20.0

License

GPL (>= 2)

Maintainer

Mauro Castro

Last Published

February 15th, 2017

Functions in RedeR (1.20.0)

addLegend

Add graph legends to RedeR application.
addSeries

Add series to RedeR application.
addEdges

Add edges to RedeR graphs.
getContainerComponets

Get container components.
RedPort

The constructor for the RedPort class.
addNodes

Add nodes to RedeR graphs.
relax

relax
resetd

Reset RedeR app.
addEdgeBetweenContainers

Add edges between containers.
getTargetEdgeIDs

Get target-edge IDs.
selectAllNodes

selectAllNodes
addSubgraph.list

Add a list of subgraphs to RedeR application.
cea

Co-expression analysis.
selectEdges

selectEdges
att

Map and set edge and vertex attributes to RedeR application.
gtoy.rm

Random graphs and modules.
deleteSelectedEdges

Delete selected edges in RedeR graphs.
getSourceEdgeIDs

Get source-edge IDs.
calld

Call RedeR app from R.
addSubgraph

Add subgraphs to RedeR application.
deleteEdges

Remove edges from RedeR graphs.
updateGraph

Update RedeR graphs.
getNodeIDs

Get node IDs.
selectGraph

Select graph.
deSelectNodes

Unmark selected nodes.
deleteNodes

Remove nodes from RedeR graphs.
mergeOutEdges

Merge out-edges between connected containers and transfers edges from nodes to containers.
setArrowDirection

Set arrow direction.
subg

Subgraph of a graph.
selectNodes

Select nodes.
isDynamicsActive

Inquires about RedeR current state.
deSelectEdges

Unmark selected edges.
exitd

Exit RedeR R-to-Java interface.
duplicateGraph

Duplicate graphs in RedeR application.
deSelectGraph

Unmark selected graph objects.
getEdges

Get edges.
mergeNodes

Merge nodes.
updateContainerSize

Update container size.
ping

Test RedeR R-to-Java interface.
RedPort-class

Class "RedPort"
getEdgeIDs

Get edge IDs.
nesthc

Nest hclust objects to containers.
version

Version
RedeR-package

RedeR: bridging the gap between network analysis and visualization.
addGraph

Add graphs to RedeR application.
getNodes

Get nodes.
RedeR.data

Pre-processed dataset for RedeR case study.
deleteSelectedNodes

Delete selected nodes in RedeR graphs.
nestNodes

Nest nodes to containers.
selectAllEdges

Select all edges.
getGraph

Get RedeR graph.