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.
getArrowDirection       Get arrow direction.
getContainerComponets   Get container components.
getEdgeColor            Get edge color.
getEdgeIDs              Get edge IDs.
getEdgeType             Get edge type.
getEdgeWeight           Get edge weight.
getEdgeWidth            Get edge width.
getEdges                Get edges.
getGraph                Get RedeR graph.
getNodeAliases          Get node aliases.
getNodeBend             Get node bend.
getNodeColor            Get node color.
getNodeFontColor        Get font color.
getNodeFontName         Get font name.
getNodeFontSize         Get font size.
getNodeFontStyle        Get font style.
getNodeFontX            Get font x coordinate.
getNodeFontY            Get font y coordinate.
getNodeH                Get node height.
getNodeIDs              Get node IDs.
getNodeLineColor        Get node-line color.
getNodeLineWidth        Get node-line width.
getNodeShape            Get node shape.
getNodeSize             Get node size.
getNodeW                Get node with.
getNodeWeight           Get node weight.
getNodeX                Get node x coordinate.
getNodeY                Get node y coordinate.
getNodes                Get nodes.
getSourceEdgeIDs        Get source-edge IDs.
getSourceEdges          Get source edges.
getTargetEdgeIDs        Get target-edge IDs.
getTargetEdges          getTargetEdges
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.
setEdgeColor            Set edge color.
setEdgeType             Set edge type.
setEdgeWeight           Set edge weight.
setEdgeWidth            Set edge width.
setNodeAlias            Set node alias.
setNodeBend             Set node bend.
setNodeColor            Set node color.
setNodeFontColor        Set font color.
setNodeFontName         Set font name.
setNodeFontSize         Set font size.
setNodeFontStyle        Set font style.
setNodeFontXY           Set font x,y coordinates.
setNodeLineColor        Set node-line color.
setNodeLineWidth        Set node-line width.
setNodeShape            Set node shape.
setNodeSize             Set node size.
setNodeWeight           Set node weight.
setNodeXY               Set node x,y coordinates.
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
