improve as.igraph (165f14c7) · Commits · github_fork / LinkET

NAMESPACE

+0 −1

Original line number	Diff line number	Diff line
		@@ -191,7 +191,6 @@ importFrom(gtable,gtable_row)
		importFrom(gtable,gtable_width)
		importFrom(igraph,V)
		importFrom(igraph,as.igraph)
		importFrom(igraph,graph_from_data_frame)
		importFrom(igraph,vertex_attr)
		importFrom(magrittr,"%>%")
		importFrom(purrr,map_dbl)

R/network.R

+42 −10

Original line number	Diff line number	Diff line
		#' @title Coerce to a Graph
		#' @description Functions to coerce a object to graph if possible.
		#' @param x any \code{R} object.
		#' @param use_adjacency logical, if TRUE will build graph from adjacency matrix.
		#' @param diag logical, if TRUE will keep the diagonal of adjacency matrix data.
		#' @param simplify if TRUE, Simple graphs are graphs which do not contain loop
		#' and multiple edges.
		#' @param directed whether or not to create a directed graph.
		#' @param ... other parameters.
		#' @return a graph object.
		#' @importFrom igraph graph_from_data_frame
		#' @importFrom igraph as.igraph
		#' @importFrom tidygraph as_tbl_graph
		#' @author Hou Yun
		#' @rdname network
		as.igraph.cor_md_tbl <- function(x,
		...,
		use_adjacency = FALSE,
		diag = FALSE,
		simplify = TRUE,
		directed = FALSE) {
		rnm <- row_names(x)
		cnm <- col_names(x)
		x <- dplyr::filter(x, ...)
		params <- list(...)
		if (is.null(params)) {
		gparams <- list()
		} else {
		gparams <- params[names(params) != ""]
		params <- unname(params[names(params) == ""])
		}
		x <- do.call(dplyr::filter, c(list(.data = x), params))

		if (isFALSE(use_adjacency)) {
		if(isTRUE(simplify)) {
		if(identical(rnm, cnm) && isFALSE(directed)) {
		x <- extract_upper(x, FALSE)
		x <- extract_upper(x, diag)
		}
		nodes <- unique(c(x$.rownames, x$.colnames))
		} else {
		nodes <- unique(c(rnm, cnm))
		}
		graph_from_data_frame(x, directed = directed, vertices = nodes)
		igraph::graph_from_data_frame(x, directed = directed, vertices = nodes)
		} else {
		if(isTRUE(simplify)) {
		if(identical(rnm, cnm) && isFALSE(directed)) {
		x <- extract_upper(x, diag)
		}
		}

		if (isTRUE(directed)) {
		mode <- "directed"
		} else {
		if (isTRUE(simplify)) {
		mode <- "max"
		} else {
		mode <- "undirected"
		}
		}

		do.call(igraph::graph_from_adjacency_matrix,
		c(list(adjmatrix = adjacency_matrix(x),
		mode = mode, diag = diag, weighted = TRUE), gparams))
		}
		}

		#' @rdname network
		@@ -104,7 +136,7 @@ adjacency_matrix.cor_md_tbl <- function(x, ...) {

		#' @method adjacency_matrix default
		adjacency_matrix.default <- function(x, ...) {
		adjacency_matrix(as_md_tbl(x), ...)
		adjacency_matrix(as_md_tbl(x, ...))
		}

		#' @noRd

man/network.Rd

+12 −1

Original line number	Diff line number	Diff line
		@@ -15,7 +15,14 @@
		\alias{as_tbl_graph.corr.test}
		\title{Coerce to a Graph}
		\usage{
		\method{as.igraph}{cor_md_tbl}(x, ..., simplify = TRUE, directed = FALSE)
		\method{as.igraph}{cor_md_tbl}(
		x,
		...,
		use_adjacency = FALSE,
		diag = FALSE,
		simplify = TRUE,
		directed = FALSE
		)

		\method{as.igraph}{correlate}(x, ...)

		@@ -44,6 +51,10 @@

		\item{...}{other parameters.}

		\item{use_adjacency}{logical, if TRUE will build graph from adjacency matrix.}

		\item{diag}{logical, if TRUE will keep the diagonal of adjacency matrix data.}

		\item{simplify}{if TRUE, Simple graphs are graphs which do not contain loop
		and multiple edges.}

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