deprecate fast_correlate() and anno_link() (3c41005d) · Commits · github_fork / LinkET

R/correlate.R

+1 −20

Original line number	Diff line number	Diff line
		@@ -18,6 +18,7 @@
		#' @details The columns of 'x' will be tested for each pair when y is NULL(the default),
		#' otherwise each column in 'x' and each column in 'y' is tested for each pair.
		#' @return a list with correlation matrix, P values matrix, confidence intervals matrix.
		#' @note `fast_correlate()` and `fast_correlate2()` has been deprecated in 0.0.4 version.
		#' @importFrom stats cor cor.test p.adjust p.adjust.methods
		#' @importFrom purrr walk2
		#' @rdname correlate
		@@ -208,26 +209,6 @@ correlate <- function(x,
		)
		}

		#' @rdname correlate
		#' @export
		fast_correlate <- function(...)
		{
		## Note: will be removed in next version
		warning("fast_correlate() is soft deprecated,\n",
		"please use correlate() instead.", call. = FALSE)
		correlate(..., engine = "WGCNA")
		}

		#' @rdname correlate
		#' @export
		fast_correlate2 <- function (...)
		{
		## Note: will be removed in next version
		warning("fast_correlate2() is soft deprecated,\n",
		"please use correlate() instead.", call. = FALSE)
		correlate(..., engine = "picante")
		}

		#' Print correlate object.
		#' @param all if FALSE (default) just print correlation matrix, else will
		#' print all values.

0 → 100644

+27 −0

Original line number	Diff line number	Diff line
		#' @rdname correlate
		#' @export
		fast_correlate <- function(...)
		{
		stop("fast_correlate() is soft deprecated,\n",
		"please use correlate(..., engine = \"WGCNA\") instead.",
		call. = FALSE)
		}

		#' @rdname correlate
		#' @export
		fast_correlate2 <- function (...)
		{
		## Note: will be removed in next version
		stop("fast_correlate2() is soft deprecated,\n",
		"please use correlate(..., engine = \"picante\") instead.",
		call. = FALSE)
		}

		#' @rdname geom_couple
		#' @export
		anno_link <- function(...) {
		## Note: will be removed in next version
		stop("`anno_link()` has been deprecated,\n",
		"please use `geom_couple()` instead.",
		call. = FALSE)
		}

+1 −10

Original line number	Diff line number	Diff line
		@@ -8,7 +8,7 @@
		#' @param offset_x,offset_y NULL or named-list, add a little offset to the node points.
		#' @param ... extra parameters passing to layer function.
		#' @return a ggplot layer.
		#' @note `anno_link()` has been soft deprecated, please use `geom_couple()`
		#' @note `anno_link()` has been deprecated in 0.0.4, please use `geom_couple()`
		#' instead.
		#' @importFrom ggplot2 geom_segment
		#' @importFrom ggplot2 geom_text
		@@ -42,15 +42,6 @@ geom_couple <- function(data,
		class = "geom_couple")
		}

		#' @rdname geom_couple
		#' @export
		anno_link <- function(...) {
		## Note: will be removed in next version
		warning("`anno_link()` has been deprecated,\n",
		"please use `geom_couple()` instead.", call. = FALSE)
		geom_couple(...)
		}

		#' @importFrom ggplot2 aes_
		#' @importFrom ggplot2 ggplot_add
		#' @importFrom ggplot2 expand_limits

+10 −7

Original line number	Diff line number	Diff line
		% Generated by roxygen2: do not edit by hand
		% Please edit documentation in R/correlate.R
		% Please edit documentation in R/correlate.R, R/deprecated.R
		\name{correlate}
		\alias{correlate}
		\alias{fast_correlate}
		\alias{fast_correlate2}
		\alias{print.correlate}
		\alias{print.grouped_correlate}
		\alias{fast_correlate}
		\alias{fast_correlate2}
		\title{Correlate}
		\usage{
		correlate(
		@@ -20,13 +20,13 @@ correlate(
		...
		)

		fast_correlate(...)

		fast_correlate2(...)

		\method{print}{correlate}(x, all = FALSE, ...)

		\method{print}{grouped_correlate}(x, all = FALSE, ...)

		fast_correlate(...)

		fast_correlate2(...)
		}
		\arguments{
		\item{x, y}{a matrix object or NULL.}
		@@ -63,6 +63,9 @@ Matrix of Correlations, P-values and confidence intervals
		The columns of 'x' will be tested for each pair when y is NULL(the default),
		otherwise each column in 'x' and each column in 'y' is tested for each pair.
		}
		\note{
		`fast_correlate()` and `fast_correlate2()` has been deprecated in 0.0.4 version.
		}
		\examples{
		correlate(mtcars)

+8 −8

Original line number	Diff line number	Diff line
		% Generated by roxygen2: do not edit by hand
		% Please edit documentation in R/geom-couple.R
		\name{geom_couple}
		\alias{geom_couple}
		% Please edit documentation in R/deprecated.R, R/geom-couple.R
		\name{anno_link}
		\alias{anno_link}
		\alias{geom_couple}
		\alias{nice_curvature}
		\title{Link Layer}
		\usage{
		anno_link(...)

		geom_couple(
		data,
		mapping = NULL,
		@@ -20,11 +22,11 @@ geom_couple(
		...
		)

		anno_link(...)

		nice_curvature(curvature, by = "to")
		}
		\arguments{
		\item{...}{extra parameters passing to layer function.}

		\item{data}{a data frame.}

		\item{mapping}{aesthetic mappings parameters.}
		@@ -37,8 +39,6 @@ nice_curvature(curvature, by = "to")

		\item{offset_x, offset_y}{NULL or named-list, add a little offset to the node points.}

		\item{...}{extra parameters passing to layer function.}

		\item{curvature}{a numeric value giving the amount of curvature.}

		\item{by}{one of "from" or "to". Compute the best curvature based on
		@@ -51,7 +51,7 @@ a ggplot layer.
		Function to draw mantel test plot on a correlation matrix heatmap.
		}
		\note{
		`anno_link()` has been soft deprecated, please use `geom_couple()`
		`anno_link()` has been deprecated in 0.0.4, please use `geom_couple()`
		instead.
		}
		\author{