Package: graph 1.83.0
Bioconductor Package Maintainer
graph: graph: A package to handle graph data structures
A package that implements some simple graph handling capabilities.
Authors:
graph_1.83.0.tar.gz
graph_1.83.0.zip(r-4.5)graph_1.83.0.zip(r-4.4)graph_1.83.0.zip(r-4.3)
graph_1.83.0.tgz(r-4.4-arm64)graph_1.83.0.tgz(r-4.4-x86_64)graph_1.83.0.tgz(r-4.3-arm64)graph_1.83.0.tgz(r-4.3-x86_64)
graph_1.83.0.tar.gz(r-4.5-noble)graph_1.83.0.tar.gz(r-4.4-noble)
graph_1.83.0.tgz(r-4.4-emscripten)graph_1.83.0.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-1.83.0(bioc 3.20)graph-1.82.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:4602e2657a
Exports:.dropEdges.ftM2otheraccaddEdgeaddNodeadjadjacencyMatrixaM2bpGattrDataItemattrDataItem<-attrDefaultsattrDefaults<-aveNumEdgesboundarybuildRepDepGraphcalcProbcalcSumProbclearNodeclusteringCoefficientcoercecombineNodescomplementconnCompdegreeDFSDistdumpGXLduplicatedEdgesedgeDataedgeData<-edgeDataDefaultsedgeDataDefaults<-edgeLedgeMatrixedgemodeedgemode<-edgeNamesedgeRenderInfoedgeRenderInfo<-edgesedgeSetIntersect0edgeSetsedgeSetUnion0edgeWeightseweightseWVextractFromToextractGraphAMextractGraphBAMfromGXLftM2adjMftM2graphNELftM2intgraph.pargraph.par.getgraph2SparseMgraphAMgraphBAMgraphIntersectgraphNELgraphRenderInfographRenderInfo<-graphUniongxlTreeNELinEdgesinitializeint2ftMintersectionintersection2isAdjacentisConnectedisDirectedjoinleaveslistEdgesmgEdgeDatamgEdgeData<-mgEdgeDataDefaultsmgEdgeDataDefaults<-mostEdgesMultiGraphnodeDatanodeData<-nodeDataDefaultsnodeDataDefaults<-nodeRenderInfonodeRenderInfo<-nodesnodes<-numEdgesnumNodesnumNoEdgesparRenderInfoparRenderInfo<-pathWeightsplotrandomEGraphrandomGraphrandomNodeGraphremoveAttrDataItem<-removeEdgeremoveEdgesByWeightremoveNodereverseEdgeDirectionsshowsparseM2GraphsubGraphsubsetEdgeSetsthresholdtoDotRtoDotWithRItoGXLugraphugraphOldunionupdateGraphvalidateGXLvalidGraph
Dependencies:BiocGenerics
Attributes for Graph Objects
Rendered fromgraphAttributes.Rmdusingknitr::rmarkdownon Jul 03 2024.Last update: 2023-09-28
Started: 2023-09-28
How To use the clusterGraph and distGraph classes
Rendered fromclusterGraph.Rmdusingknitr::rmarkdownon Jul 03 2024.Last update: 2024-04-18
Started: 2023-02-24
Graph Design
Rendered fromGraphClass.Rmdusingknitr::rmarkdownon Jul 03 2024.Last update: 2022-10-28
Started: 2022-10-28
graphBAM and MultiGraph classes
Rendered fromMultiGraphClass.Rmdusingknitr::rmarkdownon Jul 03 2024.Last update: 2022-12-07
Started: 2022-12-07
How to use the graph package
Rendered fromgraph.Rmdusingknitr::rmarkdownon Jul 03 2024.Last update: 2024-04-18
Started: 2023-03-27
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 |
