From 7e5681d3d48275f8cafedd4799298efaf2b4c1d4 Mon Sep 17 00:00:00 2001 From: stemangiola Date: Mon, 26 Jun 2023 19:33:02 +1000 Subject: [PATCH] fix docs --- R/methods.R | 9 ++++++++- man/layer_arrow_down-method.Rd | 6 ++++-- man/layer_arrow_up-method.Rd | 6 ++++-- man/layer_asterisk-method.Rd | 6 ++++-- man/layer_diamond-method.Rd | 6 ++++-- man/layer_point-method.Rd | 6 ++++-- man/layer_square-method.Rd | 6 ++++-- man/layer_star-method.Rd | 6 ++++-- man/layer_text-method.Rd | 2 +- 9 files changed, 37 insertions(+), 16 deletions(-) diff --git a/R/methods.R b/R/methods.R index e5ccc5e..e9cac27 100644 --- a/R/methods.R +++ b/R/methods.R @@ -648,6 +648,7 @@ setMethod("annotation_bar", "InputHeatmap", function(.data, #' #' @param .data A `InputHeatmap` #' @param ... Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept. +#' @param .size A column name or a double. The size of the elements of the layer. #' #' #' @details It uses `ComplexHeatmap` as visualisation tool. @@ -701,6 +702,7 @@ setMethod("layer_arrow_up", "InputHeatmap", function(.data,..., #' #' @param .data A `InputHeatmap` #' @param ... Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept. +#' @param .size A column name or a double. The size of the elements of the layer. #' #' #' @details It uses `ComplexHeatmap` as visualisation tool. @@ -753,6 +755,7 @@ setMethod("layer_arrow_down", "InputHeatmap", function(.data,..., #' #' @param .data A `InputHeatmap` #' @param ... Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept. +#' @param .size A column name or a double. The size of the elements of the layer. #' #' #' @details It uses `ComplexHeatmap` as visualisation tool. @@ -805,6 +808,7 @@ setMethod("layer_point", "InputHeatmap", function(.data,..., #' #' @param .data A `InputHeatmap` #' @param ... Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept. +#' @param .size A column name or a double. The size of the elements of the layer. #' #' #' @details It uses `ComplexHeatmap` as visualisation tool. @@ -856,6 +860,7 @@ setMethod("layer_square", "InputHeatmap", function(.data,..., #' #' @param .data A `InputHeatmap` #' @param ... Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept. +#' @param .size A column name or a double. The size of the elements of the layer. #' #' #' @details It uses `ComplexHeatmap` as visualisation tool. @@ -908,6 +913,7 @@ setMethod("layer_diamond", "InputHeatmap", function(.data,..., #' #' @param .data A `InputHeatmap` #' @param ... Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept. +#' @param .size A column name or a double. The size of the elements of the layer. #' #' #' @details It uses `ComplexHeatmap` as visualisation tool. @@ -960,6 +966,7 @@ setMethod("layer_star", "InputHeatmap", function(.data,..., #' #' @param .data A `InputHeatmap` #' @param ... Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept. +#' @param .size A column name or a double. The size of the elements of the layer. #' #' #' @details It uses `ComplexHeatmap` as visualisation tool. @@ -1016,7 +1023,7 @@ setMethod("layer_asterisk", "InputHeatmap", function(.data,..., #' @param .data A `InputHeatmap` #' @param ... Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept. #' @param .value A column name or character string. -#' @param .size A column name or a double. +#' @param .size A column name or a double. The size of the elements of the layer. #' #' #' @details It uses `ComplexHeatmap` as visualisation tool. diff --git a/man/layer_arrow_down-method.Rd b/man/layer_arrow_down-method.Rd index cb59df8..ee18a99 100644 --- a/man/layer_arrow_down-method.Rd +++ b/man/layer_arrow_down-method.Rd @@ -6,14 +6,16 @@ \alias{layer_arrow_down,InputHeatmap-method} \title{Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} \usage{ -layer_arrow_down(.data, .size = NULL, ...) +layer_arrow_down(.data, ..., .size = NULL) -\S4method{layer_arrow_down}{InputHeatmap}(.data, .size = NULL, ...) +\S4method{layer_arrow_down}{InputHeatmap}(.data, ..., .size = NULL) } \arguments{ \item{.data}{A `InputHeatmap`} \item{...}{Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept.} + +\item{.size}{A column name or a double. The size of the elements of the layer.} } \value{ A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` diff --git a/man/layer_arrow_up-method.Rd b/man/layer_arrow_up-method.Rd index 03338a4..4e776f9 100644 --- a/man/layer_arrow_up-method.Rd +++ b/man/layer_arrow_up-method.Rd @@ -6,14 +6,16 @@ \alias{layer_arrow_up,InputHeatmap-method} \title{Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} \usage{ -layer_arrow_up(.data, .size = NULL, ...) +layer_arrow_up(.data, ..., .size = NULL) -\S4method{layer_arrow_up}{InputHeatmap}(.data, .size = NULL, ...) +\S4method{layer_arrow_up}{InputHeatmap}(.data, ..., .size = NULL) } \arguments{ \item{.data}{A `InputHeatmap`} \item{...}{Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept.} + +\item{.size}{A column name or a double. The size of the elements of the layer.} } \value{ A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` diff --git a/man/layer_asterisk-method.Rd b/man/layer_asterisk-method.Rd index 4e4fe87..ca9df52 100644 --- a/man/layer_asterisk-method.Rd +++ b/man/layer_asterisk-method.Rd @@ -6,14 +6,16 @@ \alias{layer_asterisk,InputHeatmap-method} \title{Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} \usage{ -layer_asterisk(.data, .size = NULL, ...) +layer_asterisk(.data, ..., .size = NULL) -\S4method{layer_asterisk}{InputHeatmap}(.data, .size = NULL, ...) +\S4method{layer_asterisk}{InputHeatmap}(.data, ..., .size = NULL) } \arguments{ \item{.data}{A `InputHeatmap`} \item{...}{Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept.} + +\item{.size}{A column name or a double. The size of the elements of the layer.} } \value{ A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` diff --git a/man/layer_diamond-method.Rd b/man/layer_diamond-method.Rd index 54b0657..819b924 100644 --- a/man/layer_diamond-method.Rd +++ b/man/layer_diamond-method.Rd @@ -6,14 +6,16 @@ \alias{layer_diamond,InputHeatmap-method} \title{Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} \usage{ -layer_diamond(.data, .size = NULL, ...) +layer_diamond(.data, ..., .size = NULL) -\S4method{layer_diamond}{InputHeatmap}(.data, .size = NULL, ...) +\S4method{layer_diamond}{InputHeatmap}(.data, ..., .size = NULL) } \arguments{ \item{.data}{A `InputHeatmap`} \item{...}{Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept.} + +\item{.size}{A column name or a double. The size of the elements of the layer.} } \value{ A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` diff --git a/man/layer_point-method.Rd b/man/layer_point-method.Rd index 38e65e3..f5dc615 100644 --- a/man/layer_point-method.Rd +++ b/man/layer_point-method.Rd @@ -6,14 +6,16 @@ \alias{layer_point,InputHeatmap-method} \title{Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} \usage{ -layer_point(.data, .size = NULL, ...) +layer_point(.data, ..., .size = NULL) -\S4method{layer_point}{InputHeatmap}(.data, .size = NULL, ...) +\S4method{layer_point}{InputHeatmap}(.data, ..., .size = NULL) } \arguments{ \item{.data}{A `InputHeatmap`} \item{...}{Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept.} + +\item{.size}{A column name or a double. The size of the elements of the layer.} } \value{ A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` diff --git a/man/layer_square-method.Rd b/man/layer_square-method.Rd index 19e08aa..96577d4 100644 --- a/man/layer_square-method.Rd +++ b/man/layer_square-method.Rd @@ -6,14 +6,16 @@ \alias{layer_square,InputHeatmap-method} \title{Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} \usage{ -layer_square(.data, .size = NULL, ...) +layer_square(.data, ..., .size = NULL) -\S4method{layer_square}{InputHeatmap}(.data, .size = NULL, ...) +\S4method{layer_square}{InputHeatmap}(.data, ..., .size = NULL) } \arguments{ \item{.data}{A `InputHeatmap`} \item{...}{Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept.} + +\item{.size}{A column name or a double. The size of the elements of the layer.} } \value{ A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` diff --git a/man/layer_star-method.Rd b/man/layer_star-method.Rd index 7ac1240..7399a10 100644 --- a/man/layer_star-method.Rd +++ b/man/layer_star-method.Rd @@ -6,14 +6,16 @@ \alias{layer_star,InputHeatmap-method} \title{Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} \usage{ -layer_star(.data, .size = NULL, ...) +layer_star(.data, ..., .size = NULL) -\S4method{layer_star}{InputHeatmap}(.data, .size = NULL, ...) +\S4method{layer_star}{InputHeatmap}(.data, ..., .size = NULL) } \arguments{ \item{.data}{A `InputHeatmap`} \item{...}{Expressions that return a logical value, and are defined in terms of the variables in .data. If multiple expressions are included, they are combined with the & operator. Only rows for which all conditions evaluate to TRUE are kept.} + +\item{.size}{A column name or a double. The size of the elements of the layer.} } \value{ A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` diff --git a/man/layer_text-method.Rd b/man/layer_text-method.Rd index d903167..8132036 100644 --- a/man/layer_text-method.Rd +++ b/man/layer_text-method.Rd @@ -17,7 +17,7 @@ layer_text(.data, ..., .value, .size = NULL) \item{.value}{A column name or character string.} -\item{.size}{A column name or a double.} +\item{.size}{A column name or a double. The size of the elements of the layer.} } \value{ A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap`