RedeR: Interactive visualization and manipulation of nested networks

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RedeR")
AuthorMauro Castro, Xin Wang, Florian Markowetz
Bioconductor views DataRepresentation GraphAndNetwork Infrastructure Network Software Visualization
Date of publicationNone
MaintainerMauro Castro <mauro.a.castro@gmail.com>
LicenseGPL (>= 2)
Version1.24.0
http://genomebiology.com/2012/13/4/R29

View on Bioconductor

Man pages

addEdgeBetweenContainers: Add edges between containers.

addEdges: Add edges to RedeR graphs.

addGraph: Add graphs to RedeR application.

addLegend: 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: Map and set edge and vertex attributes to RedeR application.

calld: Call RedeR app from R.

cea: Co-expression analysis.

deleteEdges: Remove edges from RedeR graphs.

deleteNodes: Remove nodes from RedeR graphs.

deleteSelectedEdges: Delete selected edges in RedeR graphs.

deleteSelectedNodes: Delete selected nodes in RedeR graphs.

deSelectEdges: Unmark selected edges.

deSelectGraph: Unmark selected graph objects.

deSelectNodes: Unmark selected nodes.

duplicateGraph: Duplicate graphs in RedeR application.

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...

nesthc: Nest hclust objects to containers.

nestNodes: Nest nodes to containers.

ping: Test RedeR R-to-Java interface.

RedeR.data: Pre-processed dataset for RedeR case study.

RedeR-package: RedeR: bridging the gap between network analysis and...

RedPort: The constructor for the RedPort class.

RedPort-class: Class "RedPort"

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.

updateContainerSize: Update container size.

updateGraph: Update RedeR graphs.

version: Version

Functions

addEdgeBetweenContainers Man page
addEdgeBetweenContainers,RedPort-method Man page
addEdges Man page
addEdges,RedPort-method Man page
addGraph Man page
addGraph,RedPort-method Man page
addLegend.color Man page
addLegend.color,RedPort-method Man page
addLegend.shape Man page
addLegend.shape,RedPort-method Man page
addLegend.size Man page
addLegend.size,RedPort-method Man page
addNodes Man page
addNodes,RedPort-method Man page
addSeries Man page
addSeries,RedPort-method Man page
addSubgraph Man page
addSubgraph.list Man page
addSubgraph.list,RedPort-method Man page
addSubgraph,RedPort-method Man page
att.mape Man page
att.mapv Man page
att.sete Man page
att.setv Man page
calld Man page
calld,RedPort-method Man page
Carroll2006 Man page
cea Man page
deleteEdges Man page
deleteEdges,RedPort-method Man page
deleteNodes Man page
deleteNodes,RedPort-method Man page
deleteSelectedEdges Man page
deleteSelectedEdges,RedPort-method Man page
deleteSelectedNodes Man page
deleteSelectedNodes,RedPort-method Man page
deSelectEdges Man page
deSelectEdges,RedPort-method Man page
deSelectGraph Man page
deSelectGraph,RedPort-method Man page
deSelectNodes Man page
deSelectNodes,RedPort-method Man page
duplicateGraph Man page
duplicateGraph,RedPort-method Man page
ER.deg Man page
ER.limma Man page
exitd Man page
exitd,RedPort-method Man page
getContainerComponets Man page
getContainerComponets,RedPort-method Man page
getEdgeIDs Man page
getEdgeIDs,RedPort-method Man page
getEdges Man page
getEdges,RedPort-method Man page
getGraph Man page
getGraph,RedPort-method Man page
getNodeIDs Man page
getNodeIDs,RedPort-method Man page
getNodes Man page
getNodes,RedPort-method Man page
getSourceEdgeIDs Man page
getSourceEdgeIDs,RedPort-method Man page
getTargetEdgeIDs Man page
getTargetEdgeIDs,RedPort-method Man page
gtoy.rm Man page
hs.inter Man page
isDynamicsActive Man page
isDynamicsActive,RedPort-method Man page
mergeNodes Man page
mergeNodes,RedPort-method Man page
mergeOutEdges Man page
mergeOutEdges,RedPort-method Man page
nesthc Man page
nesthc,RedPort-method Man page
nestNodes Man page
nestNodes,RedPort-method Man page
ping Man page
ping,RedPort-method Man page
RedeR Man page
RedeR-package Man page
RedPort Man page
RedPort-class Man page
relax Man page
relax,RedPort-method Man page
resetd Man page
resetd,RedPort-method Man page
selectAllEdges Man page
selectAllEdges,RedPort-method Man page
selectAllNodes Man page
selectAllNodes,RedPort-method Man page
selectEdges Man page
selectEdges,RedPort-method Man page
selectGraph Man page
selectGraph,RedPort-method Man page
selectNodes Man page
selectNodes,RedPort-method Man page
setArrowDirection Man page
setArrowDirection,RedPort-method Man page
subg Man page
updateContainerSize Man page
updateContainerSize,RedPort-method Man page
updateGraph Man page
updateGraph,RedPort-method Man page
version Man page
version,RedPort-method Man page

Files

.Rinstignore
DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllGenerics.R R/AllMethods.R R/RedPort.R R/Supplements.R R/zzz.R
build
build/vignette.rds
data
data/Carroll2006.RData
data/ER.deg.RData
data/ER.limma.RData
data/datalist
data/hs.inter.RData
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/RedeR.R
inst/doc/RedeR.Rnw
inst/doc/RedeR.pdf
inst/java
inst/java/reder_v2.jar
inst/script
inst/script/script_case_st.r
man
man/RedPort-class.Rd man/RedPort.Rd man/RedeR-package.Rd man/RedeR.data.Rd man/addEdgeBetweenContainers.Rd man/addEdges.Rd man/addGraph.Rd man/addLegend.Rd man/addNodes.Rd man/addSeries.Rd man/addSubgraph.Rd man/addSubgraph.list.Rd man/att.Rd man/calld.Rd man/cea.Rd man/deSelectEdges.Rd man/deSelectGraph.Rd man/deSelectNodes.Rd man/deleteEdges.Rd man/deleteNodes.Rd man/deleteSelectedEdges.Rd man/deleteSelectedNodes.Rd man/duplicateGraph.Rd man/exitd.Rd man/getContainerComponets.Rd man/getEdgeIDs.Rd man/getEdges.Rd man/getGraph.Rd man/getNodeIDs.Rd man/getNodes.Rd man/getSourceEdgeIDs.Rd man/getTargetEdgeIDs.Rd man/gtoy.rm.Rd man/isDynamicsActive.Rd man/mergeNodes.Rd man/mergeOutEdges.Rd man/nestNodes.Rd man/nesthc.Rd man/ping.Rd man/relax.Rd man/resetd.Rd man/selectAllEdges.Rd man/selectAllNodes.Rd man/selectEdges.Rd man/selectGraph.Rd man/selectNodes.Rd man/setArrowDirection.Rd man/subg.Rd man/updateContainerSize.Rd man/updateGraph.Rd man/version.Rd
vignettes
vignettes/RedeR.Rnw
vignettes/bib.bib
vignettes/fig1.pdf
vignettes/fig2.pdf
vignettes/fig3.pdf
vignettes/fig4.pdf
vignettes/fig5a.pdf
vignettes/fig5b.pdf
vignettes/fig5c.pdf
vignettes/fig6.pdf
vignettes/fig7.pdf

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