Carroll2006             Pre-processed dataset for RedeR case study.
PluginBuilder           The constructor for the PluginBuilder class.
PluginBuilder-class     Class 'PluginBuilder'
RedPort                 The constructor for the RedPort class.
RedPort-class           Class "RedPort"
RedeR-package           RedeR: bridging the gap between network
                        analysis and visualization.
addEdgeBetweenContainers
                        Add edges between containers.
addEdges                Add edges to RedeR graphs.
addGraph                Add graphs to RedeR application.
addLegend.color         Add graph legends to RedeR application.
addNodes                Add nodes to RedeR graphs.
addSeries               Add series to RedeR application.
addSubgraph             Add subgraphs to RedeR application.
addSubgraph.list        Add a list of subgraphs to RedeR application.
att.setv                Map and set edge and vertex attributes to RedeR
                        application.
calld                   Call RedeR app from R.
cea                     Co-expression analysis.
deSelectEdges           Unmark selected edges.
deSelectGraph           Unmark selected graph objects.
deSelectNodes           Unmark selected nodes.
deleteEdges             Remove edges from RedeR graphs.
deleteNodes             Remove nodes from RedeR graphs.
deletePlugin            Remove plugins from RedeR application.
deleteSelectedEdges     Delete selected edges in RedeR graphs.
deleteSelectedNodes     Delete selected nodes in RedeR graphs.
duplicateGraph          Duplicate graphs in RedeR application.
dynwin                  Wrap R graphics.
exitd                   Exit RedeR R-to-Java interface.
getContainerComponets   Get container components.
getEdgeIDs              Get edge IDs.
getEdges                Get edges.
getGraph                Get RedeR graph.
getNodeIDs              Get node IDs.
getNodes                Get nodes.
getSourceEdgeIDs        Get source-edge IDs.
getTargetEdgeIDs        Get target-edge IDs.
gtoy.rm                 Random graphs and modules.
isDynamicsActive        Inquires about RedeR current state.
mergeNodes              Merge nodes.
mergeOutEdges           Merge out-edges between connected containers
                        and transfers edges from nodes to containers.
nestNodes               Nest nodes to containers.
nesthc                  Nest hclust objects to containers.
ping                    Test RedeR R-to-Java interface.
pluginParser            RedeR plugin parser.
rederpost               Remote procedure calls optimized for RedeR.
relax                   relax
resetd                  Reset RedeR app.
selectAllEdges          Select all edges.
selectAllNodes          selectAllNodes
selectEdges             selectEdges
selectGraph             Select graph.
selectNodes             Select nodes.
setArrowDirection       Set arrow direction.
subg                    Subgraph of a graph.
submitPlugin            Submit plugins to RedeR application.
updateContainerSize     Update container size.
updateGraph             Update RedeR graphs.
updatePlugins           Update RedeR plugins.
version                 Version
