matrix2Graph: Coercions between matrix and graph representations

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

Coercions between matrix and graph representations

Description

A collection of functions and methods to convert various forms of matrices into graph objects.

Usage

aM2bpG(aM)
ftM2adjM(ft, W=NULL, V=NULL, edgemode="directed")
ftM2graphNEL(ft, W=NULL, V=NULL, edgemode="directed")
## S4 method for signature 'graphNEL,matrix'
coerce(from,to="matrix",strict=TRUE)
## S4 method for signature 'matrix,graphNEL'
coerce(from,to="graphNEL",strict=TRUE)

Arguments

ft	An nx2 matrix containing the from/to representation of graph edges.
W	An optional vector of edge weights.
V	An optional vector of node names.
aM	An affiliation matrix for a bipartite graph.
edgemode	Character. Specifies if the resulting graph is to be directed or undirected.
from	Object to coerce from, either of type matrix or grpahNEL
to	Character giving class to coerce to. Either "matrix" or "graphNEL".
strict	Strict object checking.

Details

In the functions ftM2adjM and ftM2graphNEL, a from/to matrix ft is converted into an adjacency matrix or a graphNEL object respectively. In ft, the first column represents the from nodes and the second column the to nodes.

To have unconnected nodes, use the V argument (see below). The edgemode parameter can be used to specify if the desired output is a directed or undirected graph.

The same edge must not occur twice in the from/to matrix. If edgemode is undirected, the edge (u,v) and (v,u) must only be specified once.

W is an optional vector of edge weights. The order of the edge weights in the vector should correspond to the order of the edges recorded in ft. If it is not specified, edge weights of 1 are assigned by default.

V is an optional vector of node names. All elements of ft must be contained in V, but not all names in V need to be contained in ft. If V is not specified, it is set to all nodes represented in ft. Specifying V is most useful for creating a graph that includes nodes with degree 0.

aM is an affiliation matrix as frequently used in social networks analysis. The rows of aM represent actors, and the columns represent events. An entry of "1" in the ith row and jth column represents affiliation of the ith actor with the jth event. Weighted entries may also be used. aM2bpG returns a graphNEL object with nodes consisting of the set of actors and events, and directed (possibly weighted) edges from the actors to their corresponding events. If plotted using Rgraphviz and the dot layout, the bipartite structure of the graph returned by aM2bpG should be evident.

An adjacency matrix can be coerced into a graphNEL using the as method. If the matrix is a symmetric matrix, then the resulting graph will be undirected, otherwise it will be directed.

Value

For ftM2graphNEL and aM2bpG, an object of class graphNEL. For ftM2adjM, a matrix (the adjacency matrix representation).

Author(s)

Denise Scholtens, Wolfgang Huber

Examples

## From-To matrix

From <- c("A","A","C","C")
To   <- c("B","C","B","D")
L <- cbind(From,To)

W  <- 1:4
M1 <- ftM2adjM(L, W, edgemode="directed")
M2 <- ftM2adjM(L, W, edgemode="undirected")
stopifnot(all(M1+t(M1)==M2))

G1 <- ftM2graphNEL(L, W, edgemode="directed")
G2 <- ftM2graphNEL(L, W, edgemode="undirected")

## Adjacency matrix

From <- matrix(runif(100), nrow=10, ncol=10)
From <- (From+t(From)) > pi/4
rownames(From) <- colnames(From) <- LETTERS[1:10]

To <- as(From,"graphNEL")
Back <- as(To,"matrix")

stopifnot(all(From == Back))

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