# matrix2Graph: Coercions between matrix and graph representations In Bioconductor/graph: graph: A package to handle graph data structures

## Description

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

## Usage

 ```1 2 3 4 5 6 7``` ```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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24``` ```## 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 May 31, 2021, 8:28 p.m.