gRbase (version 1.8-3.4)

graph-xxx2yyy: Graph, matrix and generating class coercions

Description

Graph and matrix coercions where speed is an issue.

Usage

graphNEL2M(gn, result = "matrix")
graphNEL2MAT(gn, limit = 100)
graphNEL2ftM(gn)
graphNEL2tfM(gn)
graphNEL2igraph(gn)
M2igraph(amat)
M2graphNEL(amat)
M2adjList(amat)
M2ugList(amat)
M2dagList(amat)
ugList2graphNEL(glist, vn = NULL)
ugList2M(glist, vn = NULL, result = "matrix")
dagList2graphNEL(glist, vn = NULL)
dagList2M(glist, vn = NULL, result = "matrix")
adjList2M(alist, result = "matrix")
dagList2tfM(glist)
as.adjMAT(gn, result = "matrix")
ug2dag(gn)
MAT2matrix(mat)
MAT2dgCMatrix(mat)

Arguments

gn

A graphNEL object

result

Either "matrix" or "dgCMatrix" (for a sparse matrix representation)

limit

If number of nodes is larger than limit, the result will be a sparse dgCMatrix; otherwise a dense matrix.

amat

Adjacency matrix

glist

A list of generators where a generator is a character vector. If interpreted as generators of an undirected graph, a generator is a complete set of vertices in the graph. If interpreted as generators of a dag, a generator (v1,...,vn) means that there will be arrows from v2,...,vn to v1.

vn

The names of the vertices in the graphs. These will be the row and column names of the matrix

alist

An adjacency list.

mat

Either a dense matrix or a sparse dgCMatrix.

Value

An adjacency matrix (or NULL if glist has length 0)

See Also

ug, dag

Examples

# NOT RUN {
glist <- list(1:3, 2:4, 4:5)
am1 <- ugList2M( glist )
am2 <- dagList2M( glist )
if (interactive()){
  plot(as(am1, "graphNEL"))
  plot(as(am2, "graphNEL"))
}


## Sparse and dense adjacency matrices converted to igraph
g1 <- ug(~a:b + b:c + c:d, result="matrix")
g2 <- ug(~a:b + b:c + c:d, result="dgCMatrix")
plot( M2igraph( g1 ) )
plot( M2igraph( g2 ) )

## Sparse and dense adjacency matrices converted to graphNEL
g1 <- ug(~a:b + b:c + c:d, result="matrix")
g2 <- ug(~a:b + b:c + c:d, result="dgCMatrix")
M2graphNEL( g1 )
M2graphNEL( g2 )

## Sparse and dense adjacency matrices converted to adjacency list 
g1 <- ug(~a:b + b:c + c:d, result="matrix")
g2 <- ug(~a:b + b:c + c:d, result="dgCMatrix")
M2adjList( g1 )
## M2adjList( g2 ) FAILS for sparse matrix

## Sparse and dense adjacency matrices converted to cliques
g1 <- ug(~a:b + b:c + c:d, result="matrix")
g2 <- ug(~a:b + b:c + c:d, result="dgCMatrix")
M2ugList( g1 )
M2ugList( g2 ) 

## Sparse and dense adjacency matrices converted to cliques
g1 <- ug(~a:b + b:c + c:d, result="matrix")
g2 <- ug(~a:b + b:c + c:d, result="dgCMatrix")
M2dagList( g1 )
## M2dagList( g2 ) ## Fails for sparse matrix

g1 <- dag(~a:b + b:c + c:d, result="matrix")
g2 <- dag(~a:b + b:c + c:d, result="dgCMatrix")
M2dagList( g1 )
## M2dagList( g2 ) ## FIXME Fails for sparse matrix

# }