R/matrix2graph.R

In gMCP: Graph Based Multiple Comparison Procedures

#' Matrix2Graph and Graph2Matrix
#' 
#' Creates a graph of class \code{\link{graphMCP}} from a given transition
#' matrix or vice versa.
#' 
#' The hypotheses names are the row names or if these are \code{NULL}, the
#' column names or if these are also \code{NULL} of type H1, H2, H3, ...
#' 
#' If the diagonal of the matrix is unequal zero, the values are ignored and a
#' warning is given.
#' 
#' @aliases matrix2graph graph2matrix
#' @param m A transition matrix.
#' @param weights A numeric for the initial weights.
#' @param graph A graph of class \code{\link{graphMCP}}.
#' @return A graph of class \code{\link{graphMCP}} with the given transition
#' matrix for matrix2graph.  The transition matrix of a \code{\link{graphMCP}}
#' graph for graph2matrix.
#' @author Kornelius Rohmeyer \email{rohmeyer@@small-projects.de}
#' @keywords graphs
#' @examples
#' 
#' 
#' # Bonferroni-Holm:
#' m <- matrix(rep(1/3, 16), nrow=4)
#' diag(m) <- c(0, 0, 0, 0)
#' graph <- matrix2graph(m)
#' print(graph)
#' graph2matrix(graph)
#' 
#' 
#' @export matrix2graph

matrix2graph <- function(m, weights=rep(1/dim(m)[1],dim(m)[1])) {
	# Checking for 0 on diagonal:
	if (!(all(TRUE == all.equal(unname(diag(m)), rep(0, length(diag(m)))))
	   || all(TRUE == all.equal(unname(diag(m)), rep("0", length(diag(m))))))) {
		warning("Matrix has a diagonal not equal to zero. Loops are not allowed.")
		diag(m) <- rep(0, length(diag(m)))
	}
	# Creating graph without edges:
	if (dim(m)[1]!=dim(m)[2]) stop("Matrix has to be quadratic.")
	hnodes <- rownames(m)
	if (is.null(hnodes)) hnodes <- colnames(m)
	if (is.null(hnodes)) hnodes <- paste("H",1:(dim(m)[1]),sep="")
	rownames(m) <- colnames(m) <- hnodes
	graph <- new("graphMCP", m=m, weights=weights)
	return(graph)
}

#' @rdname matrix2graph
#' @export graph2matrix
graph2matrix <- function(graph) {
	if (class(graph) %in% "graphMCP") {
		return(graph@m)
	} else if (class(graph) %in% "entangledMCP"){
		# TODO What do we want to return in this case?
		warning("graph2matrix only returns the transition matrix of the first subgraph.")
		return(graph@subgraphs[[1]]@m)
	} else {
		stop("This function should only be used for objects of class graphMCP or entangledMCP.")
	}
}