add diag params to remove self-links (c782ea9e) · Commits · github_fork / LinkET

R/network.R

+8 −1

Original line number	Diff line number	Diff line
		@@ -132,11 +132,12 @@ as_tbl_graph.corr.test <- function(x, ...) {
		#' @description Can be used to convert a correlation object to adjacency matrix.
		#' @param x a correlation object (\code{correlate}, \code{md_tbl}, and so on).
		#' @param ... expressions that return a logical value.
		#' @param diag if FALSE (default), self-edges will be removed.
		#' @return a matrix object.
		#' @author Hou Yun
		#' @rdname adjacency_matrix
		#' @export
		adjacency_matrix <- function(x, ...) {
		adjacency_matrix <- function(x, ..., diag = FALSE) {
		if (!inherits(x, "cor_md_tbl") && !inherits(x, "correlate")) {
		clss <- class(x)[1]
		x <- as_md_tbl(x)
		@@ -150,6 +151,9 @@ adjacency_matrix <- function(x, ...) {
		}
		rnm <- row_names(x)
		cnm <- col_names(x)
		if (isFALSE(diag) && identical(rnm, cnm)) {
		x <- trim_diag(x)
		}
		x <- dplyr::filter(x, ...)
		out <- df_to_matrix(x, "r", row_id = ".rownames", col_id = ".colnames",
		row_names = rnm, col_names = cnm, missing = 0)
		@@ -166,6 +170,9 @@ adjacency_matrix <- function(x, ...) {
		x$r[!id] <- 0
		}
		out <- x$r
		if (isFALSE(diag) && identical(rownames(out), colnames(out))) {
		diag(out) <- 0
		}
		}
		out
		}

+3 −1

Original line number	Diff line number	Diff line
		@@ -4,12 +4,14 @@
		\alias{adjacency_matrix}
		\title{Generate adjacency matrix}
		\usage{
		adjacency_matrix(x, ...)
		adjacency_matrix(x, ..., diag = FALSE)
		}
		\arguments{
		\item{x}{a correlation object (\code{correlate}, \code{md_tbl}, and so on).}

		\item{...}{expressions that return a logical value.}

		\item{diag}{if FALSE (default), self-edges will be removed.}
		}
		\value{
		a matrix object.