combineNodes: combineNodes

In Bioconductor/graph: graph: A package to handle graph data structures

combineNodes

Description

A function to combine, or collapse, a specified set of nodes in a graph.

Usage

combineNodes(nodes, graph, newName, ...)
## S4 method for signature 'character,graphNEL,character'
combineNodes(nodes, graph, newName, collapseFunction=sum)

Arguments

nodes	A set of nodes that are to be collapsed.
graph	The graph containing the nodes
newName	The name for the new, collapsed node.
collapseFunction	Function or character giving the name of a function used to collapse the edge weights after combining nodes. The default is to sum up the weights, but mean would be a useful alternative.
...	Additional arguments for the generic

Details

The nodes specified are reduced to a single new node with label given by newName. The in and out edges of the set of nodes are all made into in and out edges for the new node.

Value

An new instance of a graph of the same class as graph is returned. This new graph has the specified nodes reduced to a single node.

Author(s)

R. Gentleman

See Also

inEdges, addNode

Examples

  V <- LETTERS[1:4]
  edL1 <- vector("list", length=4)
  names(edL1) <- V
  for(i in 1:4)
    edL1[[i]] <- list(edges=c(2,1,4,3)[i], weights=sqrt(i))
  gR <- graphNEL(nodes=V, edgeL=edL1, edgemode="directed")
  gR <- addNode("M", gR)
  gR <- addEdge("M", "A", gR, 1)
  gR <- addEdge("B", "D", gR, 1)
  gX <- combineNodes(c("B","D"), gR, "X")

  gR <- addNode("K", gR)
  gR <- addEdge(c("K","K"), c("D", "B"), gR, c(5,3))
  edgeWeights(combineNodes(c("B","D"), gR, "X"))$K
  edgeWeights(combineNodes(c("B","D"), gR, "X", mean))$K

Bioconductor/graph documentation built on Nov. 2, 2024, 7:25 a.m.