R: Conversions "graph" <-> (sparse) Matrix

graph-sparseMatrix {Matrix}

R Documentation

Conversions "graph" <–> (sparse) Matrix

Description

The Matrix package has supported conversion from and to "graph" objects from (Bioconductor) package graph since summer 2005, via the usual as(., "<class>") coercion,

  as(from, Class)

Since 2013, this functionality is further exposed as the graph2T() and T2graph() functions (with further arguments than just from), which convert graphs to and from the triplet form of sparse matrices (of class "TsparseMatrix") .

Usage

graph2T(from, use.weights = )
T2graph(from, need.uniq = is_not_uniqT(from), edgemode = NULL)

Arguments

`from`	for `graph2T()`, an R object of class `"graph"`; for `T2graph()`, a sparse matrix inheriting from `"TsparseMatrix"`.
`use.weights`	logical indicating if weights should be used, i.e., equivalently the result will be numeric, i.e. of class `dgTMatrix`; otherwise the result will be `ngTMatrix` or `nsTMatrix`, the latter if the graph is undirected. The default looks if there are weights in the graph, and if any differ from `1`, weights are used.
`need.uniq`	a logical indicating if `from` may need to be internally “uniqified”; do not set this and hence rather use the default, unless you know what you are doing!
`edgemode`	one of `NULL`, `"directed"`, or `"undirected"`. The default `NULL` looks if the matrix is symmetric and assumes `"undirected"` in that case.

Value

For graph2T(), a sparse matrix inheriting from "TsparseMatrix".

For T2graph() an R object of class "graph".

Examples

if(isTRUE(try(require(graph)))) { ## super careful .. for "checking reasons"
  n4 <- LETTERS[1:4]; dns <- list(n4,n4)
  show(a1 <- sparseMatrix(i= c(1:4),   j=c(2:4,1),   x = 2,    dimnames=dns))
  show(g1 <- as(a1, "graph")) # directed
  unlist(edgeWeights(g1)) # all '2'

  show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))
  show(g2 <- as(a2, "graph")) # directed
  # now if you want it undirected:
  show(g3  <- T2graph(as(a2,"TsparseMatrix"), edgemode="undirected"))
  show(m3 <- as(g3,"Matrix"))
  show( graph2T(g3) ) # a "pattern Matrix" (nsTMatrix)

  a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), giveC=FALSE) # no 'x'
  show(a.) # "ngTMatrix"
  show(g. <- as(a., "graph"))

}