graph-class {graph} | R Documentation

## Class "graph"

### Description

A virtual class that all graph classes should extend.

### Details

`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.

### Objects from the Class

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

### Slots

`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.

### Methods

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` 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.

### Author(s)

R. Gentleman and E. Whalen.

### References

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

### See Also

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

### Examples

      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'

[Package graph version 1.58.2 Index]