Description Usage Arguments Constructors Extends Methods for graphBAM objects Coercion Author(s) Examples
The graphBAM class represents a graph as an adjacency matrix. The
adjacency matrix is stored as a bit array using a raw
vector to
reduce the memory footprint and speed operations like
graphIntersection
. This class is EXPERIMENTAL and its API is
subject to change.
1 
df 
A 
nodes 
A character vector of node labels. Use this to add degree zero
nodes to the graph. If 
edgemode 
A string, one of "directed" or "undirected". 
ignore_dup_edges 
If 
The GraphBAM
function is used to create new graphBAM
instances. Edges are specified in a data.frame
. For
undirected graphs, reciprical edges should not be includes unless
ignoe_dup_edges
is TRUE
.
Class "graph"
, directly.
addEdge(from, to, graph, weights)
Return a new graphBAM
object with the specified edge(s)
added. The from
and to
arguments must either be the
same length or one of them must be of length one. Each time an
edge is added, the entire graph is copied. For the purpose of
building a graph it will often be more efficient to build up the
list of edges and call GraphBAM
.
addNode(node, object)
Return a new graphBAM
object with the specified node(s)
added.
clearNode(node, object)
This operation is not currently supported.
edges(object, which)
Returns an adjacency list representation of the graph. The list
will have an entry for each node with a vector of adjacent node
labels or character(0)
. For undirected graphs,
edges
returns the reciprocal edges. The optional
argument which
can be a character vector of node labels.
When present, only entries for the specified nodes will be
returned.
inEdges(node, object)
(Not yet supported)
Similar to the edges
function, but the adjacency list maps
nodes that have an edge to the given node instead of from the
given node.
isAdjacent(object, from, to)
Returns a logical vector indicating whether there is an edge
corresponding to the elements in from
and to
. These
vectors must have the same length, unless one has length one.
nodes(object)
Return the node labels for the graph
numEdges(object)
Returns the number of edges in the graph.
numNodes(object)
Returns the number of nodes in the graph
removeEdge(from, to, graph)
Return a new graphBAM
object with the specified edges
removed. The from
and to
arguments must be
the same length unless one of them has length one.
removeNode(node, object)
Returns a new graphBAM
object with the specified node removed.
Node and edge attributes corresponding to that node are also removed.
edgeData(self, from, to, attr)
Access edge attributes. See help for edgeData
.
edgeDataDefaults(self, attr)
Access edge data default attributes .
nodeDataDefaults(self, attr)
Access node data default attributes .
edgeWeights(object, index)
Return the edge weights for the graph in adjacency list format.
The optional argument index
specified a character vector of
nodes. In this case, only the weights for the specified nodes
will be returned.
extractFromTo(g)
Returns a data frame with column names "from", "to", and "weight" corresponding to the connected nodes in the graphBAM object.
graphIntersect(x, y, nodeFun, edgeFun)
When given two graphBAM
objects, graphIntersect
returns a new graphBAM
containing the nodes and edges in
common between the two graphs. Both x and y should either be
directed or undirected. The intersection is computed by
first finding the intersection of the node sets, obtaining the
resulting subgraphs, and finding the intersection of the resulting
edge sets. Node/Edge attributes that are equal are carried over to
the result. Non equal edge/node attributes will result in the
corresponding attribute being set to NA. The user has the option
of providing a named list of functions correspoding to the names of
the edge attributes for resolving conflicting edge attributes.
For resolving any of the conflicting node attributes
the user has the option of providing a named list
of functions
corresponding to the node attribute names.
graphUnion(x, y, nodeFun, edgeFun)
When given two graphBAM
objects, graphUnion
returns a new graphBAM
containing the union of nodes and
edges between the two graphs. The union is compted by first finding
the union of the nodesets. Both x and y should be either directed or
undirected. Node/Edge attributes that are equal are carried over to
the result. Non equal edge/node attributes will result in the
corresponding attribute being set to NA. The user has the option
of providing a named list of functions correspoding to the names of
the edge attributes for resolving conflicting edge attributes.
For resolving any of the conflicting node attributes
the user has the option of providing a named list
of functions
corresponding to the node attribute names.
edgemode(object) < value
Set the edgemode for the graph ("directed" or "undirected"). If
the specified edgemode is the same, the object is returned without
changes. Otherwise, a directed graph is converted to an
undirected graph via ugraph
and an undirected graph is
returned such that each edge is interpreted as two edges, one in
each direction.
ugraph(graph)
Return an undirected version of the current graph. Conceptually, the arrows of a graph's directed edges are removed.
nodes(object) < value
Replacement of a graphBAM
object's node labels is currently
not supported. An error is raised if this method is called.
graphBAM
objects can be coerced to graphAM
,
graphNEL
, and matrix
instances via as(g, CLASS)
.
N. Gopalakrishnan, S. Falcon
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27  f < c("a", "a", "b", "c", "d")
t < c("b", "c", "c", "d", "a")
weight < c(2.3, 2.3, 4.3, 1.0, 3.0)
df < data.frame(from=f, to=t, weight= weight, stringsAsFactors = TRUE)
g < graphBAM(df)
nd < nodes(g)
nodeDataDefaults(g, attr ="color") < "green"
nodeData(g,n=c("b", "c"), attr ="color") < "red"
w1 < edgeWeights(g)
w2 < edgeWeights(g,"a")
w3 < edgeWeights(g,1)
d1 < edges(g)
d2 < edges(g,c("a", "b"))
e1 < edgeData(g)
e2 < edgeData(g, "a", "c",attr="weight")
em < edgeMatrix(g)
id < isDirected(g)
sg < subGraph(c("a","c","d"), g)
ft < extractFromTo(g)
am < as(g,"graphAM")
nl < as(g,"graphNEL")
mt < as(g,"matrix")
k < graphIntersect(g,g)
k < graphUnion(g,g)
e < removeEdgesByWeight(g,lessThan= 3.0)
f < removeNode("a", g)
g

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