improve adjacency_matrix() (ef084c72) · Commits · github_fork / LinkET

R/network.R

+20 −3

Original line number	Diff line number	Diff line
		@@ -132,12 +132,18 @@ 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 type one of "full", "upper" or "lower", used to extract upper or lower
		#' triangular part of a adjacency matrix.
		#' @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, ..., diag = FALSE) {
		adjacency_matrix <- function(x,
		...,
		type = "full",
		diag = FALSE) {
		type <- match.arg(type, c("full", "upper", "lower"))
		if (!inherits(x, "cor_md_tbl") && !inherits(x, "correlate")) {
		clss <- class(x)[1]
		x <- as_md_tbl(x)
		@@ -154,10 +160,14 @@ adjacency_matrix <- function(x, ..., diag = FALSE) {
		if (isFALSE(diag) && identical(rnm, cnm)) {
		x <- trim_diag(x)
		}
		if (!identical(type, "full") && identical(rnm, cnm)) {
		x <- do.call(paste0("extract_", type), list(md = 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)
		} else {
		out <- x$r
		params <- rlang::enquos(...)
		if (length(params) >= 1) {
		for (ii in seq_along(params)) {
		@@ -167,12 +177,19 @@ adjacency_matrix <- function(x, ..., diag = FALSE) {
		id <- id & rlang::eval_tidy(params[[ii]], x)
		}
		}
		x$r[!id] <- 0
		out[!id] <- 0
		}
		out <- x$r

		if (isFALSE(diag) && identical(rownames(out), colnames(out))) {
		diag(out) <- 0
		}
		if (!identical(type, "full") && identical(rownames(out), colnames(out))) {
		.f <- switch (type,
		"upper" = "lower.tri",
		"lower" = "upper.tri"
		)
		out[do.call(.f, list(x = out))] <- 0
		}
		}
		out
		}

man/adjacency_matrix.Rd

+4 −1

Original line number	Diff line number	Diff line
		@@ -4,13 +4,16 @@
		\alias{adjacency_matrix}
		\title{Generate adjacency matrix}
		\usage{
		adjacency_matrix(x, ..., diag = FALSE)
		adjacency_matrix(x, ..., type = "full", diag = FALSE)
		}
		\arguments{
		\item{x}{a correlation object (\code{correlate}, \code{md_tbl}, and so on).}

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

		\item{type}{one of "full", "upper" or "lower", used to extract upper or lower
		triangular part of a adjacency matrix.}

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

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