R/ptr.R

In youngser/gmmase: Graph Spectral Clustering

#'
#' Run pass-to-rank on a weighted graph.
#'
#' It extracts (non-zero) edge weight vector \eqn{W} from a graph and replaces it with \eqn{2*R / (|E|+1)} where \eqn{R} is the rank of \eqn{W} and \eqn{|E|} is the number of edges. This does 'no-op' for an unweighted graph.
#'
#' @param g a graph in \code{igraph} format or an n x 2 edge list or an n x n adjacency matrix
#'
#' @author Youngser Park <youngser@jhu.edu>
#' @export
#' @import igraph

ptr <- function(g)
{
    if (class(g) != "igraph") {
        if (!is.matrix(g)) stop("the input has to be either an igraph object or a matrix!")
        else {
            if (ncol(g)==2) g <- graph_from_edgelist(g)
            else if (nrow(g)==ncol(g)) g <- graph_from_adjacency_matrix(g, weighted = TRUE)
            else stop("the input matrix is not a graph format!")
        }
    }

    if (is.weighted(g)) {
        W <- E(g)$weight
    } else { # no-op!
        W <- rep(1,ecount(g))
    }

    E(g)$weight <- rank(W)*2 / (ecount(g)+1)
    return(g)
}