graph-class: Class "graph"
In pshannon-bioc/graph: graph: A package to handle graph data structures

Description Details Objects from the Class Slots Methods Author(s) References See Also Examples

A virtual class that all graph classes should extend.

degree returns either a named vector (names correspond to the nodes in the graph) containing the degree for undirected graphs or a list with two components, inDegree and outDegree for directed graphs.

connComp returns a list of the connected components. Each element of this list contains the labels of all nodes in that component.

For a directed graph or digraph the underlying graph is the graph that results from removing all direction from the edges. This can be achieved using the function ugraph.

A weakly connected component of a digraph is one that is a connected component of the underlying graph. This is the default for connComp. A digraph is strongly connected if every two vertices are mutually reachable. A strongly connected component of a digraph, D, is a maximal strongly connected subdigraph of D. See the RBGL package for an implementation of Trajan's algorithm to find strongly connected components (strongComp).

In the graph implementation of connComp weak connectivity is used. If the argument to connComp is a directed graph then ugraph is called to create the underlying undirected graph and that is used to compute connected components. Users who want different behavior are encouraged to use RBGL.

A virtual Class: No objects may be created from it.

edgeData:: An attrData instance for edge attributes.
nodeData:: An attrData instance for node attributes.
graphData:: A list for graph-level attributes. Only mandatory list item is edgemode which indicates whether edges are "directed" or "undirected"
renderInfo:: A list of graph rendering information.

nodes: return a character vector containing the names of the nodes of the graph
nodes<-: rename the nodes of the graph
show: signature(object = "graph"):A print method for the graph.
acc: signature(object = "graph"): find all nodes accessible from the specified node.
complement: signature(x = "graph"): compute the complement of the supplied graph. The complement is defined with respect to the complete graph on the nodes in x. Currently this returns an object of class graphNEL.
connComp: signature(object = "graph"): find the connected components of a graph.
degree: signature(object = "graph", Nodes = "missing"): find the degree of a node (number of coincident edges).
degree: signature(object = "graph", Nodes = "ANY"): as above.
degree: signature(object = "MultiGraph", Nodes = "missing"): find the degree of a node (number of coincident edges).
dfs: signature(object = "graph"): execute a depth first search on a graph starting with the specified node.
edges: signature(object="graph", which="character"): return the edges indicated by which. which can be missing in which case all edges are returned or it can be a character vector with the node labels indicating the nodes whose edge lists are wanted.
edgeDataDefaults: Get and set default attributes for the edges in the graph.
edgeData: Get and set attributes for edges in the graph
edgemode: signature(object="graph"): return the edgemode for the graph. Currently this can be either directed or undirected.
edgemode<-: signature(object="graph", value="character"): set the edgemode for the graph. Currently this can be either directed or undirected.
edgeWeights: Return a list of edge weights in a list format similar to the edges method.
intersection: signature(x = "graph", y = "graph"): compute the intersection of the two supplied graphs. They must have identical nodes. Currently this returns an object of class graphNEL. With edge weights of 1 for any matching edge.
isAdjacent: signature(from="character", to="character"): Determine if edges exists between nodes.
isConnected: signature(object = "graph"): A boolean that details if a graph is fully connected or not.
isDirected: Return TRUE if the graph object has directed edges and FALSE otherwise.
join: signature(x = "graph", y = "graph"): returns the joining of two graphs. Nodes which are shared by both graphs will have their edges merged. Note that edgeWeights for the resulting graph are all set to 1. Users wishing to preserve weights in a join operation must perform addEdge operations on the resulting graph to restore weights.
nodes<-: A generic function that allows different implementations of the graph class to reset the node labels
nodeDataDefaults: Get/set default attributes for nodes in the graph.
nodeData: Get/set attributes for nodes in the graph.
numEdges: signature(object = "graph"): compute the number of edges in a graph.
numNodes: signature(object = "graph"): compute the number of nodes in a graph.
plot: Please see the help page for the plot.graph method in the Rgraphviz package
union: signature(x = "graph", y = "graph"): compute the union of the two supplied graphs. They must have identical nodes. Currently this returns an object of class graphNEL.
edgeNames: signature(object = "graph"): Returns a vector of the edge names for this graph, using the format tail\~head, where head is the name of the tail node and head is the name of the head node.
updateGraph: signature(object = "graph"): Updates old instances of graph objects.

R. Gentleman and E. Whalen.

Graph Theory and its Applications, J. Gross and J. Yellen.

graphNEL-class, graphAM-class, distGraph-class.

  set.seed(123)
  g1 <- randomGraph(letters[1:10], 1:4, p= 0.3)
  numEdges(g1)
  edgeNames(g1)
  edges(g1)
  edges(g1, c("a","d")) # those incident to 'a' or 'd'