Package: graph 1.85.0

Bioconductor Package Maintainer

graph: graph: A package to handle graph data structures

A package that implements some simple graph handling capabilities.

Authors:R Gentleman [aut], Elizabeth Whalen [aut], W Huber [aut], S Falcon [aut], Jeff Gentry [aut], Paul Shannon [aut], Halimat C. Atanda [ctb], Paul Villafuerte [ctb], Aliyu Atiku Mustapha [ctb], Bioconductor Package Maintainer [cre]

graph_1.85.0.tar.gz
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graph_1.85.0.tar.gz(r-4.5-noble)graph_1.85.0.tar.gz(r-4.4-noble)
graph_1.85.0.tgz(r-4.4-emscripten)graph_1.85.0.tgz(r-4.3-emscripten)
graph.pdf |graph.html✨
graph/json (API)

# Install 'graph' in R:

install.packages('graph', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

IMCAAttrs - KEGG Integrin Mediated Cell Adhesion graph
IMCAGraph - KEGG Integrin Mediated Cell Adhesion graph
MAPKsig - A graph encoding parts of the MAPK signaling pathway
MAPKsig - A graph encoding parts of the MAPK signaling pathway
apopGraph - KEGG apoptosis pathway graph
biocRepos - A graph representing the Bioconductor package repository
esetsFemale - MultiGraph edgeSet data
esetsMale - MultiGraph edgeSet data
graphExamples - A List Of Example Graphs
pancrCaIni - A graph encoding parts of the pancreatic cancer initiation pathway

On BioConductor:graph-1.85.0(bioc 3.21)graph-1.84.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

graphandnetwork

11.57 score 341 packages 796 scripts 31k downloads 45 mentions 118 exports 2 dependencies

Last updated 2 months agofrom:eff9ecd703. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win-x86_64	NOTE	Nov 29 2024
R-4.5-linux-x86_64	NOTE	Nov 29 2024
R-4.4-win-x86_64	NOTE	Nov 29 2024
R-4.4-mac-x86_64	NOTE	Nov 29 2024
R-4.4-mac-aarch64	NOTE	Nov 29 2024
R-4.3-win-x86_64	NOTE	Nov 29 2024
R-4.3-mac-x86_64	NOTE	Nov 29 2024
R-4.3-mac-aarch64	NOTE	Nov 29 2024

Exports:.dropEdges .ftM2other acc addEdge addNode adj adjacencyMatrix aM2bpG attrDataItem attrDataItem<-attrDefaults attrDefaults<-aveNumEdges boundary buildRepDepGraph calcProb calcSumProb clearNode clusteringCoefficient coerce combineNodes complement connComp degree DFS Dist dumpGXL duplicatedEdges edgeData edgeData<-edgeDataDefaults edgeDataDefaults<-edgeL edgeMatrix edgemode edgemode<-edgeNames edgeRenderInfo edgeRenderInfo<-edges edgeSetIntersect0 edgeSets edgeSetUnion0 edgeWeights eweights eWV extractFromTo extractGraphAM extractGraphBAM fromGXL ftM2adjM ftM2graphNEL ftM2int graph.par graph.par.get graph2SparseM graphAM graphBAM graphIntersect graphNEL graphRenderInfo graphRenderInfo<-graphUnion gxlTreeNEL inEdges initialize int2ftM intersection intersection2 isAdjacent isConnected isDirected join leaves listEdges mgEdgeData mgEdgeData<-mgEdgeDataDefaults mgEdgeDataDefaults<-mostEdges MultiGraph nodeData nodeData<-nodeDataDefaults nodeDataDefaults<-nodeRenderInfo nodeRenderInfo<-nodes nodes<-numEdges numNodes numNoEdges parRenderInfo parRenderInfo<-pathWeights plot randomEGraph randomGraph randomNodeGraph removeAttrDataItem<-removeEdge removeEdgesByWeight removeNode reverseEdgeDirections show sparseM2Graph subGraph subsetEdgeSets threshold toDotR toDotWithRI toGXL ugraph ugraphOld union updateGraph validateGXL validGraph

Dependencies:BiocGenerics generics

Attributes for Graph Objects

Seth Falcon, Paul Villafuerte

Rendered fromgraphAttributes.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-09-28
Started: 2023-09-28

How To use the clusterGraph and distGraph classes

Robert Gentleman, Jeff Gentry, Seth Falcon, Paul Villafuerte

Rendered fromclusterGraph.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-04-18
Started: 2023-02-24

Graph Design

R. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon, Halimat C. Atanda

Rendered fromGraphClass.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-10-28
Started: 2022-10-28

graphBAM and MultiGraph classes

N. Gopalakrishnan, Halimat C. Atanda

Rendered fromMultiGraphClass.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-12-07
Started: 2022-12-07

How to use the graph package

Robert Gentleman, Seth Falcon, Jeff Gentry, Paul Shannon, Aliyu Atiku Mustapha

Rendered fromgraph.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-04-18
Started: 2023-03-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Methods for Accessibility Lists	acc acc,clusterGraph,character-method acc,clusterGraph-method acc,graph,character-method acc,graph-method acc-methods
addEdge	addEdge
addNode	addNode addNode,character,distGraph,list-method addNode,character,graphBAM,missing-method addNode,character,graphNEL,list-method addNode,character,graphNEL,missing-method
Methods for finding the adjacency list for selected nodes.	adj adj-methods
Compute an Adjacency Matrix for a graphBAM object	adjacencyMatrix adjacencyMatrix,graphBAM-method
KEGG apoptosis pathway graph	apopAttrs apopGraph apopLocusLink
Class "attrData"	attrData-class attrDataItem,attrData,character,character-method attrDataItem,attrData,character,missing-method attrDataItem<-,attrData,character,character-method attrDefaults,attrData,character-method attrDefaults,attrData,missing-method attrDefaults<-,attrData,character,ANY-method attrDefaults<-,attrData,missing,list-method initialize,attrData-method names,attrData-method names<-,attrData,character-method removeAttrDataItem<- removeAttrDataItem<-,attrData,character,NULL-method
Get and set attributes values for items in an attrData object	attrDataItem attrDataItem-methods attrDataItem<- attrDataItem<--methods
Get and set the default attributes of an attrData object	attrDefaults attrDefaults-methods attrDefaults<- attrDefaults<--methods
Calculate the average number of edges in a graph	aveNumEdges
A graph representing the Bioconductor package repository	biocRepos
Returns the Boundary between a Graph and a SubGraph	boundary
Calculate the hypergeometric probability of the subgraph's number of edges.	calcProb
Calculate the probability that a subgraph has an unusual number of edges.	calcSumProb
clearNode	clearNode
Class "clusterGraph"	adj,clusterGraph,ANY-method clusterGraph-class coerce,clusterGraph,matrix-method connComp,clusterGraph-method edgeL,clusterGraph-method edges,clusterGraph-method edgeWeights,clusterGraph,ANY-method edgeWeights,clusterGraph-method nodes,clusterGraph-method nodes<-,clusterGraph,character-method numNodes,clusterGraph-method show,clusterGraph-method
Clustering coefficient of a graph	clusteringCoefficient clusteringCoefficient,graph clusteringCoefficient,graph-method
Coercions between matrix and graph representations	aM2bpG coerce,graphNEL,matrix-method coerce,matrix,graphNEL-method ftM2adjM ftM2graphNEL
combineNodes	combineNodes combineNodes,character,graphNEL,character-method
Depth First Search	DFS DFS,graph,character-method
Class "distGraph"	adj,distGraph,ANY-method Dist Dist,distGraph-method distGraph-class edgeL,distGraph-method edges,distGraph-method edgeWeights,distGraph,ANY-method edgeWeights,distGraph-method initialize,distGraph-method nodes,distGraph-method numNodes,distGraph-method show,distGraph-method threshold threshold,distGraph-method [.dist
duplicatedEdges	duplicatedEdges
Get and set attributes for the edges of a graph object	edgeData edgeData-methods edgeData<- edgeData<--methods
Get and set default attributes for the edges of a graph	edgeDataDefaults edgeDataDefaults-methods edgeDataDefaults<- edgeDataDefaults<--methods
Compute an Edge Matrix or weight vector for a Graph	edgeMatrix edgeMatrix,clusterGraph-method edgeMatrix,distGraph-method edgeMatrix,graphAM-method edgeMatrix,graphBAM-method edgeMatrix,graphNEL-method eWV pathWeights
MultiGraph edgeSet data	esetsFemale esetsMale
Retrieve the edge weights of a graph	edgeWeights
Methods for GXL manipulations in package graph	dumpGXL dumpGXL,connection-method dumpGXL-methods fromGXL fromGXL,connection-method fromGXL-methods GXL gxlTreeNEL NELhandler toGXL toGXL-methods validateGXL validateGXL,connection-method
Class "graph"	complement complement,graph-method connComp connComp,graph-method degree degree,graph-method degree,MultiGraph-method dfs,graph-method edgeData,graph,character,character,character-method edgeData,graph,character,character,missing-method edgeData,graph,character,missing,character-method edgeData,graph,missing,character,character-method edgeData,graph,missing,missing,character-method edgeData,graph,missing,missing,missing-method edgeData<-,graph,character,character,character,ANY-method edgeData<-,graph,character,character,character-method edgeData<-,graph,character,missing,character,ANY-method edgeData<-,graph,character,missing,character-method edgeData<-,graph,missing,character,character,ANY-method edgeData<-,graph,missing,character,character-method edgeDataDefaults,graph,character-method edgeDataDefaults,graph,missing-method edgeDataDefaults<-,graph,character,ANY-method edgeDataDefaults<-,graph,character-method edgeDataDefaults<-,graph,missing,list-method edgeL,graph-method edgemode edgemode,graph-method edgemode<- edgemode<-,graph,character-method edgeNames edgeNames,graph-method edgeWeights,graph,character-method edgeWeights,graph,missing-method edgeWeights,graph,numeric-method graph-class graphBase-class intersection intersection,graph,graph-method intersection2 intersection2,graph,graph-method isAdjacent,graph,character,character-method isConnected isConnected,graph-method isDirected,graph-method join join,graph,graph-method nodeData,graph,character,character-method nodeData,graph,character,missing-method nodeData,graph,missing,character-method nodeData,graph,missing,missing-method nodeData<-,graph,character,character-method nodeData<-,graph,missing,character-method nodeDataDefaults,graph,character-method nodeDataDefaults,graph,missing-method nodeDataDefaults<-,graph,character,ANY-method nodeDataDefaults<-,graph,character-method nodeDataDefaults<-,graph,missing,list-method nodes,graph-method nodes<-,graph,character-method numEdges numEdges,graph-method numNodes numNodes,graph-method plot,graph,ANY-method plot,graph-method show,graph-method union,graph,graph-method updateGraph updateGraph,graph-method
Defunct Functions in Package 'graph'	buildRepDepGraph graph-defunct pkgInstOrder ugraphOld
Graphical parameters and other settings	graph.par graph.par.get
Coercion methods between graphs and sparse matrices	graph2SparseM sparseM2Graph
Class "graphAM"	addEdge,character,character,graphAM,missing-method addNode,character,graphAM,missing-method clearNode,character,graphAM-method coerce,graphAM,graphBAM-method coerce,graphAM,graphNEL-method coerce,graphAM,matrix-method coerce,matrix,graphAM-method edges,graphAM-method graphAM graphAM-class inEdges,character,graphAM-method inEdges,graphAM,missing-method inEdges,missing,graphAM-method initialize,graphAM-method isAdjacent,graphAM,character,character-method nodes,graphAM-method nodes<-,graphAM,character-method numEdges,graphAM-method numNodes,graphAM-method removeEdge,character,character,graphAM-method removeNode,character,graphAM-method
EXPERIMENTAL class "graphBAM"	addEdge,character,character,graphBAM,missing-method addEdge,character,character,graphBAM,numeric-method adj,graphBAM,character-method clearNode,character,graphBAM-method coerce,graphBAM,graphAM-method coerce,graphBAM,graphNEL-method coerce,graphBAM,matrix-method edgeData,graphBAM,character,character,character-method edgeData,graphBAM,character,missing,character-method edgeData,graphBAM,missing,character,character-method edgeData,graphBAM,missing,missing,character-method edgeData,graphBAM,missing,missing,missing-method edgeData<-,graphBAM,character,character,character,ANY-method edgeData<-,graphBAM,character,character,character-method edgeData<-,graphBAM,character,missing,character,ANY-method edgeData<-,graphBAM,character,missing,character-method edgeData<-,graphBAM,missing,character,character,ANY-method edgeData<-,graphBAM,missing,character,character-method edgeData<-,graphBAM,missing,missing,character,ANY-method edgeData<-,graphBAM,missing,missing,character-method edgeDataDefaults<-,graphBAM,character,ANY-method edgeDataDefaults<-,graphBAM,missing,list-method edgemode<-,graphBAM,character-method edges,graphBAM-method edgeWeights,graphBAM,character-method edgeWeights,graphBAM,missing-method edgeWeights,graphBAM,numeric-method edgeWeights,graphBAM-method extractFromTo,graphBAM-method graphBAM graphBAM-class graphIntersect graphIntersect,graphBAM,graphBAM-method graphUnion graphUnion,graphBAM,graphBAM-method inEdges,character,graphBAM-method initialize,graphBAM-method isAdjacent,graphBAM,character,character-method nodeData,graphBAM,character,character-method nodeData,graphBAM,character,missing-method nodeData,graphBAM,missing,character-method nodeData,graphBAM,missing,missing-method nodeData<-,graphBAM,character,character-method nodeData<-,graphBAM,missing,character-method nodeDataDefaults,graphBAM,character-method nodeDataDefaults,graphBAM,missing-method nodeDataDefaults<-,graphBAM,character,ANY-method nodeDataDefaults<-,graphBAM,missing,ANY-method nodeDataDefaults<-,graphBAM,missing,list-method nodes,graphBAM-method nodes<-,graphBAM,character-method numEdges,graphBAM-method numNodes,graphBAM-method removeEdge,character,character,graphBAM-method removeEdgesByWeight removeEdgesByWeight,graphBAM-method removeNode,character,graphBAM-method show,graphBAM-method ugraph,graphBAM-method
A List Of Example Graphs	graphExamples
Class "graphNEL"	addEdge,character,character,graphNEL,missing-method addEdge,character,character,graphNEL,numeric-method addNode,character,graphNEL-method adj,graphNEL,ANY-method clearNode,character,graphNEL-method coerce coerce,graphNEL,generalGraph-method coerce,graphNEL,graphAM-method coerce,graphNEL,graphBAM-method edgeL edgeL,graphNEL-method edges edges,graphNEL-method edgeWeights,graphNEL-method graphNEL graphNEL-class inEdges,character,graphNEL-method inEdges,graphNEL,missing-method inEdges,missing,graphNEL-method initialize initialize,graphNEL-method nodes nodes,graphNEL-method nodes<- nodes<-,graphNEL,character-method numNodes,graphNEL-method removeEdge,character,character,graphNEL-method removeNode,character,graphNEL-method toGXL,graphNEL-method
Generic Method inEdges	inEdges
KEGG Integrin Mediated Cell Adhesion graph	IMCA IMCAAttrs IMCAGraph integrinMediatedCellAdhesion
Determine if nodes share an edge in a graph	isAdjacent isAdjacent-methods
Determine if a graph has directed or undirected edges	isDirected isDirected-methods
Find the leaves of a graph	leaves leaves,graph-method
List the Edges of a Graph	listEdges
A graph encoding parts of the MAPK signaling pathway	MAPKsig
Find the node in a graph with the greatest number of edges	mostEdges
Class "multiGraph"	edgemode,edgeSet-method edges,edgeSetAM-method edges,edgeSetNEL-method edges,multiGraph-method edgeSet-class edgeSetAM-class edgeSetNEL-class isDirected,edgeSet-method isDirected,multiGraph-method multiGraph-class nodes,edgeSetAM-method nodes,multiGraph-method numEdges,edgeSetAM-method numEdges,multiGraph-method numNodes,multiGraph-method show,edgeSet-method show,multiGraph-method
EXPERIMENTAL class "MultiGraph"	edgeNames,MultiGraph-method edges,MultiGraph-method edgeSetIntersect0 edgeSets edgeSets,MultiGraph-method edgeSetUnion0 eweights extractFromTo extractFromTo,MultiGraph-method extractGraphAM extractGraphBAM graphIntersect,MultiGraph,MultiGraph-method graphUnion,MultiGraph,MultiGraph-method isDirected,DiEdgeSet-method isDirected,MultiGraph-method isDirected,UEdgeSet-method mgEdgeData mgEdgeData,MultiGraph,character,character,character,character-method mgEdgeData,MultiGraph,character,character,missing,character-method mgEdgeData,MultiGraph,character,missing,character,character-method mgEdgeData,MultiGraph,character,missing,missing,character-method mgEdgeData<- mgEdgeData<-,MultiGraph,character,character,character,character-method mgEdgeData<-,MultiGraph,character,character,missing,character-method mgEdgeData<-,MultiGraph,character,missing,character,character-method mgEdgeData<-,MultiGraph,character,missing,missing,character-method mgEdgeDataDefaults mgEdgeDataDefaults,MultiGraph,character,character-method mgEdgeDataDefaults,MultiGraph,character,missing-method mgEdgeDataDefaults<- mgEdgeDataDefaults<-,MultiGraph,character,character,ANY-method mgEdgeDataDefaults<-,MultiGraph,character,missing,list-method MultiGraph MultiGraph-class nodeData,MultiGraph,character,character-method nodeData,MultiGraph,character,missing-method nodeData,MultiGraph,missing,character-method nodeData,MultiGraph,missing,missing-method nodeData<-,MultiGraph,character,character-method nodeData<-,MultiGraph,missing,character-method nodeDataDefaults,MultiGraph,character-method nodeDataDefaults,MultiGraph,missing-method nodeDataDefaults<-,MultiGraph,character,ANY-method nodeDataDefaults<-,MultiGraph,missing,list-method nodes,MultiGraph-method numEdges,MGEdgeSet-method numEdges,MultiGraph-method numNodes,MultiGraph-method show,MultiGraph-method subsetEdgeSets ugraph,DiEdgeSet-method ugraph,MultiGraph-method ugraph,UEdgeSet-method
Get and set attributes for the nodes of a graph object	nodeData nodeData-methods nodeData<- nodeData<--methods
Get and set default attributes for the nodes of a graph	nodeDataDefaults nodeDataDefaults-methods nodeDataDefaults<- nodeDataDefaults<--methods
Calculate the number of nodes that have an edge list of NULL	numNoEdges
A graph encoding parts of the pancreatic cancer initiation pathway	pancrCaIni
Random Edge Graph	randomEGraph
Random Graph	randomGraph
Generate Random Graph with Specified Degree Distribution	randomNodeGraph
removeEdge	removeEdge
removeNode	removeNode
Class "renderInfo"	edgeRenderInfo edgeRenderInfo<- graphRenderInfo graphRenderInfo<- nodeRenderInfo nodeRenderInfo<- parRenderInfo parRenderInfo<- renderInfo-class
Reverse the edges of a directed graph	reverseEdgeDirections
Class "simpleEdge".	simpleEdge-class
Standard labeling of edges with integers	ftM2int int2ftM
Create a Subgraph	subGraph subGraph,character,clusterGraph-method subGraph,character,distGraph-method subGraph,character,graphBAM-method subGraph,character,graphNEL-method subGraph,character,MultiGraph-method
Methods for Function toDotR, using R to generate a dot serialization	toDotR toDotR,graphNEL,character,list,list-method toDotR,graphNEL,character,missing,list-method toDotR,graphNEL,character,missing,missing-method toDotR,graphNEL,missing,character,missing-method toDotR,graphNEL,missing,list,list-method toDotR,graphNEL,missing,list,missing-method toDotR,graphNEL,missing,missing,list-method toDotR,graphNEL,missing,missing,missing-method
Translate a graph to "dot" including rendering information	toDotWithRI
Underlying Graph	ugraph ugraph,graph-method
Test whether graph object is valid	validGraph
Write a graph object in a file in the Tulip format	write.tlp