graph: A package to handle graph data structures

acc-methods | Methods for Accessibility Lists |

addEdge | addEdge |

addNode | addNode |

adjacencyMatrix | Compute an Adjacency Matrix for a graphBAM object |

adj-methods | Methods for finding the adjacency list for selected nodes. |

apoptosisGraph | KEGG apoptosis pathway graph |

attrData-class | Class "attrData" |

attrDataItem-methods | Get and set attributes values for items in an attrData object |

attrDefaults-methods | Get and set the default attributes of an attrData object |

aveNumEdges | Calculate the average number of edges in a graph |

biocRepos | A graph representing the Bioconductor package repository |

boundary | Returns the Boundary between a Graph and a SubGraph |

calcProb | Calculate the hypergeometric probability of the subgraph's... |

calcSumProb | Calculate the probability that a subgraph has an unusual... |

clearNode | clearNode |

clusterGraph-class | Class "clusterGraph" |

clusteringCoefficient-methods | Clustering coefficient of a graph |

combineNodes | combineNodes |

defunct | Defunct Functions in Package 'graph' |

DFS | Depth First Search |

distGraph-class | Class "distGraph" |

duplicatedEdges | duplicatedEdges |

edgeDataDefaults-methods | Get and set default attributes for the edges of a graph |

edgeData-methods | Get and set attributes for the edges of a graph object |

edgeMatrix | Compute an Edge Matrix or weight vector for a Graph |

edgeSets | MultiGraph edgeSet data |

edgeWeights | Retrieve the edge weights of a graph |

fromGXL-methods | Methods for GXL manipulations in package graph |

graph2SparseM | Coercion methods between graphs and sparse matrices |

graphAM-class | Class "graphAM" |

graphBAM-class | EXPERIMENTAL class "graphBAM" |

graph-class | Class "graph" |

graphExamples | A List Of Example Graphs |

graphNEL-class | Class "graphNEL" |

IMCA | KEGG Integrin Mediated Cell Adhesion graph |

inEdges | Generic Method inEdges |

internal | Variables used for internal purposes |

isAdjacent-methods | Determine if nodes share an edge in a graph |

isDirected-methods | Determine if a graph has directed or undirected edges |

leaves | Find the leaves of a graph |

listEdges | List the Edges of a Graph |

MAPKsig | A graph encoding parts of the MAPK signaling pathway |

matrix2Graph | Coercions between matrix and graph representations |

mostEdges | Find the node in a graph with the greatest number of edges |

multigraph | Class "multiGraph" |

MultiGraph-class | EXPERIMENTAL class "MultiGraph" |

nodeDataDefaults-methods | Get and set default attributes for the nodes of a graph |

nodeData-methods | Get and set attributes for the nodes of a graph object |

numNoEdges | Calculate the number of nodes that have an edge list of NULL |

pancrCaIni | A graph encoding parts of the pancreatic cancer initiation... |

randomEGraph | Random Edge Graph |

randomGraph | Random Graph |

randomNodeGraph | Generate Random Graph with Specified Degree Distribution |

removeEdge | removeEdge |

removeNode | removeNode |

renderInfo-class | Class "renderInfo" |

reverseEdgeDirections | Reverse the edges of a directed graph |

settings | Graphical parameters and other settings |

simpleEdge-class | Class "simpleEdge". |

standardLabeling | Standard labeling of edges with integers |

subGraph | Create a Subgraph |

toDotR-methods | Methods for Function toDotR, using R to generate a dot... |

toDotWithRI | Translate a graph to "dot" including rendering information |

ugraph | Underlying Graph |

validGraph | Test whether graph object is valid |

write.tlp | Write a graph object in a file in the Tulip format |

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