can reorder md_tbl by hc or ggtree object (f6425d7c) · Commits · github_fork / LinkET

R/reorder_by.R

+53 −9

Original line number	Diff line number	Diff line
		@@ -41,10 +41,6 @@ reorder_by.matrix <- function(x,
		by_rows <- stats::as.hclust(by_rows)
		}

		if (inherits(by_rows, "hclust") \|\| inherits(by_rows, "ggtree")) {
		attr(x, "row_tree") <- by_rows
		}

		if (inherits(by_rows, "numeric") \|\| inherits(by_rows, "character")) {
		row_ord <- by_rows
		} else {
		@@ -62,16 +58,20 @@ reorder_by.matrix <- function(x,
		by_cols <- stats::as.hclust(by_cols)
		}

		if (inherits(by_cols, "hclust") \|\| inherits(by_cols, "ggtree")) {
		attr(x, "col_tree") <- by_cols
		}

		if (inherits(by_cols, "numeric") \|\| inherits(by_cols, "character")) {
		col_ord <- by_cols
		} else {
		col_ord <- get_order(by_cols)
		}
		x[row_ord, col_ord, drop = FALSE]
		x <- x[row_ord, col_ord, drop = FALSE]

		if (inherits(by_rows, "hclust") \|\| inherits(by_rows, "ggtree")) {
		attr(x, "row_tree") <- by_rows
		}
		if (inherits(by_cols, "hclust") \|\| inherits(by_cols, "ggtree")) {
		attr(x, "col_tree") <- by_cols
		}
		x
		}

		#' @rdname reorder_by
		@@ -89,6 +89,8 @@ reorder_by.data.frame <- function(x,
		as.data.frame(x)
		}

		#' @rdname reorder_by
		#' @export
		reorder_by.correlate <- function(x,
		by_rows = "hclust",
		by_cols = by_rows,
		@@ -161,3 +163,45 @@ reorder_by.matrix_data <- function(x,
		attr(x, "col_names") <- cnm
		x
		}

		#' @rdname reorder_by
		#' @export
		reorder_by.md_tbl <- function(x,
		by_rows = NULL,
		by_cols = NULL,
		...) {
		if (inherits(by_rows, "dist")) {
		by_rows <- hclust(by_rows, ...)
		}
		if (inherits(by_rows, "dendrogram")) {
		by_rows <- stats::as.hclust(by_rows, ...)
		}
		if (inherits(by_rows, "md_tbl")) {
		by_rows <- row_names(by_rows)
		}
		if (!is.null(by_rows)) {
		if (inherits(by_rows, "hclust") \|\| inherits(by_rows, "ggtree")) {
		attr(x, "row_tree") <- by_rows
		}
		row_ord <- get_order(by_rows, name = row_names(x))
		attr(x, "row_names") <- row_names(x)[row_ord]
		}

		if (inherits(by_cols, "dist")) {
		by_cols <- hclust(by_cols, ...)
		}
		if (inherits(by_cols, "dendrogram")) {
		by_cols <- stats::as.hclust(by_cols, ...)
		}
		if (inherits(by_cols, "md_tbl")) {
		by_cols <- col_names(by_cols)
		}
		if (!is.null(by_cols)) {
		if (inherits(by_cols, "hclust") \|\| inherits(by_cols, "ggtree")) {
		attr(x, "col_tree") <- by_cols
		}
		col_ord <- get_order(by_cols, name = col_names(x))
		attr(x, "col_names") <- col_names(x)[col_ord]
		}
		x
		}

man/reorder_by.Rd

+6 −0

Original line number	Diff line number	Diff line
		@@ -4,7 +4,9 @@
		\alias{reorder_by}
		\alias{reorder_by.matrix}
		\alias{reorder_by.data.frame}
		\alias{reorder_by.correlate}
		\alias{reorder_by.matrix_data}
		\alias{reorder_by.md_tbl}
		\title{Re-sorting Matrix Data}
		\usage{
		reorder_by(x, ...)
		@@ -25,6 +27,8 @@ reorder_by(x, ...)
		...
		)

		\method{reorder_by}{correlate}(x, by_rows = "hclust", by_cols = by_rows, dist_fun = NULL, ...)

		\method{reorder_by}{matrix_data}(
		x,
		by_rows = "hclust",
		@@ -32,6 +36,8 @@ reorder_by(x, ...)
		dist_fun = dist_func(),
		...
		)

		\method{reorder_by}{md_tbl}(x, by_rows = NULL, by_cols = NULL, ...)
		}
		\arguments{
		\item{x}{matrix data.}

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