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

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

A graph class where node and edge information is represented as an adjacency matrix. The adjacency matrix is square and element adjMat[i, j] is one if there is an edge from node i to node j and zero otherwise.

The non-zero matrix values can be used to initialize an edge attribute. If this is desired, use the values argument in the call to new and provide a list with a single named element. The name determines the attributes and the value provides the default value for that attribute.

Objects can be created by calls of the form graphAM(adjMat, edgemode, values).

adjMat:: An adjacency "matrix" describing the graph structure. The colnames of the matrix will be used as node names for the graph if present.
edgeData:: Storage for edge attributes.
nodeData:: Storage for node attributes.

Class "graph", directly.

graphAM(adjMat=matrix(integer(), 0, 0), edgemode='undirected', values=NA) creates a graphAM instance.

adjMat: An integer matrix specifying which nodes have edges between them.
edgemode: Either "directed" or "undirected".
values: A named list of length 1, used (rather obscurely) to specify that non-zero adjMat values initialize an edge attribute. The name of the single element in that list becomes the name of that attribute, with the specified default value. This default value is, however, never used: the specified edge attribute always has the value contained in the adjacency matrix, which is traditionally 1, but can be any positive number.

addEdge: signature(from = "character", to = "character", graph = "graphAM", weights = "missing"): ...
addNode: signature(object = "graphAM", nodes = "character"): ...
clearNode: signature(node = "character", object = "graphAM"): ...
coerce: signature(from = "graphAM", to = "graphNEL"): ...
coerce: signature(from = "graphAM", to = "graphBAM"): ...
coerce: signature(from = "graphAM", to = "matrix"): In converting to a matrix, if an edge attribute named "weight" is defined, the non-zero elements of the matrix will contain the corresponding attribute value. For more flexible matrix conversion, see toMatrix.
coerce: signature(from = "matrix", to = "graphAM"): This coerce method exists for symmetry. In most cases, creating a new graphAM instance using new gives one more control over the resulting graph.
edges: signature(object = "graphAM", which = "missing"): ...
edges: signature(object = "graphAM", which = "character"): ...
initialize: signature(.Object = "graphAM"): ...
inEdges: signature(node = "character", object = "graphNEL"): Return the incoming edges for the specified nodes. See inEdges.
isAdjacent: signature(object = "graphAM", from = "character", to = "character"): ...
nodes<-: signature(object = "graphAM", value = "character"): ...
nodes: signature(object = "graphAM"): ...
numEdges: signature(graph = "graphAM"): ...
numNodes: signature(object = "graphAM"): ...
removeEdge: signature(from = "character", to = "character", graph = "graphAM"): ...
removeNode: signature(node = "character", object = "graphAM"): ...

Seth Falcon

graph-class, graphNEL-class

mat <- rbind(c(0, 0, 1, 1),
             c(0, 0, 1, 1),
             c(1, 1, 0, 1),
             c(1, 1, 1, 0))
rownames(mat) <- colnames(mat) <- letters[1:4]
g1 <- graphAM(adjMat=mat)
stopifnot(identical(mat, as(g1, "matrix")), validObject(g1))

## now with weights:
mat[1,3] <- mat[3,1] <- 10
gw <- graphAM(adjMat=mat, values=list(weight=1))

## consistency check:
stopifnot(identical(mat, as(gw, "matrix")),
          validObject(gw),
          identical(gw, as(as(gw, "graphNEL"), "graphAM")))