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")`

: find the`degree`

of a node (number of coincident edges).- degree
`signature(object = "MultiGraph")`

: 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.

R. Gentleman and E. Whalen.

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

`graphNEL-class`

, `graphAM-class`

,
`distGraph-class`

.

1 2 3 4 5 6 |

```
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
[1] 21
[1] "a~g" "a~i" "a~b" "a~d" "a~e" "a~f" "a~h" "b~f" "b~j" "b~d" "b~e" "b~h"
[13] "c~h" "d~e" "d~f" "d~h" "e~f" "e~h" "f~j" "f~h" "g~i"
$a
[1] "g" "i" "b" "d" "e" "f" "h"
$b
[1] "f" "j" "a" "d" "e" "h"
$c
[1] "h"
$d
[1] "a" "b" "e" "f" "h"
$e
[1] "a" "b" "d" "f" "h"
$f
[1] "b" "j" "a" "d" "e" "h"
$g
[1] "a" "i"
$h
[1] "c" "a" "b" "d" "e" "f"
$i
[1] "a" "g"
$j
[1] "b" "f"
$a
[1] "g" "i" "b" "d" "e" "f" "h"
$d
[1] "a" "b" "e" "f" "h"
```

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