merge dev

Merge branch 'dev' # Conflicts: # README.md # man/fragments/figures/unnamed-chunk-19-1.png # man/fragments/figures/unnamed-chunk-20-1.png
stemangiola · Nov 21, 2022 · da76666 · da76666
2 parents 24fc4b1 + 79de9ad
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidyHeatmap
 Title: A Tidy Implementation of Heatmap
-Version: 1.8.1
+Version: 1.9.0
 Authors@R: 
     c(person(given = "Stefano",
            family = "Mangiola",
@@ -67,5 +67,5 @@ Biarch: true
 biocViews: AssayDomain, Infrastructure
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Language: en-US
diff --git a/NAMESPACE b/NAMESPACE
@@ -5,6 +5,10 @@ export(add_bar)
 export(add_line)
 export(add_point)
 export(add_tile)
+export(annotation_bar)
+export(annotation_line)
+export(annotation_point)
+export(annotation_tile)
 export(as_ComplexHeatmap)
 export(heatmap)
 export(layer_arrow_down)

diff --git a/R/deprecated_framework.R b/R/deprecated_framework.R
@@ -462,4 +462,264 @@ annot_to_list_OLD = function(.data){
 								 	{ setNames( pull(., color),  pull(., col_name))    })
 		), ~ (.))
 
-}
+}
+
+#' DEPRECATED. Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`
+#'
+#' \lifecycle{maturing}
+#'
+#' @description add_bar() from a `InputHeatmap` object, adds a bar annotation layer.
+#'
+#' @importFrom rlang enquo
+#' @importFrom magrittr "%>%"
+#' @importFrom grid unit 
+#' 
+#'
+#' @name add_bar
+#' @rdname add_bar-method
+#'
+#' @param .data A `tbl_df` formatted as | <ELEMENT> | <FEATURE> | <VALUE> | <...> |
+#' @param .column Vector of quotes
+#' @param palette A character vector of colors, or a function such as colorRamp2 (see examples).
+#' @param size A grid::unit object, e.g. unit(2, "cm"). This is the height or width of the annotation depending on the orientation.
+#' @param ... The arguments that will be passed to top_annotation or left_annotation of the ComplexHeatmap container
+#'
+#' @details It uses `ComplexHeatmap` as visualisation tool.
+#' 
+#' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap`
+#'
+#'
+#'
+#' @examples
+#'
+#' print("DEPRECATED") 
+#'
+#'
+#' @export
+setGeneric("add_bar", function(.data,
+															 .column,
+															 palette = NULL, size = NULL,...)
+	standardGeneric("add_bar"))
+
+#' DEPRECATED. Adds a tile annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`
+#'
+#' \lifecycle{maturing}
+#'
+#' @description add_tile() from a `InputHeatmap` object, adds a tile annotation layer.
+#'
+#' @importFrom rlang enquo
+#' @importFrom magrittr "%>%"
+#' @importFrom grid unit 
+#'
+#' @name add_tile
+#' @rdname add_tile-method
+#'
+#' @param .data A `tbl_df` formatted as | <ELEMENT> | <FEATURE> | <VALUE> | <...> |
+#' @param .column Vector of quotes
+#' @param palette A character vector of colors, or a function such as colorRamp2 (see examples).
+#' @param size A grid::unit object, e.g. unit(2, "cm"). This is the height or width of the annotation depending on the orientation.
+#' @param ... The arguments that will be passed to top_annotation or left_annotation of the ComplexHeatmap container
+#'
+#' @details It uses `ComplexHeatmap` as visualisation tool.
+#' 
+#' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap`
+#'
+#'
+#'
+#' @examples
+#'
+#' print("DEPRECATED") 
+#'
+#' @export
+setGeneric("add_tile", function(.data,
+																.column,
+																palette = NULL, size = NULL, ...)
+	standardGeneric("add_tile"))
+
+#' DEPRECATED. add_tile
+#' 
+#' @docType methods
+#' @rdname add_tile-method
+#' 
+#' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap`
+#'
+setMethod("add_tile", "InputHeatmap", function(.data,
+																							 .column,
+																							 palette = NULL, size = NULL,...){
+
+	deprecate_warn("1.9.0", "tidyHeatmap::add_tile()", details = "Please use `annotation_tile()` instead")
+
+	.column = enquo(.column)
+
+	annotation_tile(.data = .data, .column = !!.column, palette = palette, size = size, ...)
+
+})
+
+#' DEPRECATED. Adds a point annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`
+#'
+#' \lifecycle{maturing}
+#'
+#' @description add_point() from a `InputHeatmap` object, adds a point annotation layer.
+#'
+#' @importFrom rlang enquo
+#' @importFrom magrittr "%>%"
+#' @importFrom grid unit 
+#' 
+#'
+#' @name add_point
+#' @rdname add_point-method
+#'
+#' @param .data A `tbl_df` formatted as | <ELEMENT> | <FEATURE> | <VALUE> | <...> |
+#' @param .column Vector of quotes
+#' @param palette A character vector of colors, or a function such as colorRamp2 (see examples).
+#' @param size A grid::unit object, e.g. unit(2, "cm"). This is the height or width of the annotation depending on the orientation.
+#' @param ... The arguments that will be passed to top_annotation or left_annotation of the ComplexHeatmap container
+#'
+#' @details It uses `ComplexHeatmap` as visualisation tool.
+#' 
+#' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap`
+#'
+#'
+#'
+#' @examples
+#'
+#' print("DEPRECATED") 
+#'
+#'
+#' @export
+setGeneric("add_point", function(.data,
+																 .column,
+																 palette = NULL, size = NULL,...)
+	standardGeneric("add_point"))
+
+#' DEPRECATED. add_point
+#' 
+#' @docType methods
+#' @rdname add_point-method
+#' 
+#' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap`
+#'
+setMethod("add_point", "InputHeatmap", function(.data,
+																								.column,
+																								palette = NULL, size = NULL,...){
+
+	.column = enquo(.column)
+
+	deprecate_warn("1.9.0", "tidyHeatmap::add_point()", details = "Please use `annotation_point()` instead")
+
+	annotation_point(.data = .data, .column = !!.column, palette = palette, size = size, ...)
+
+})
+
+#' DEPRECATED. Adds a line annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`
+#'
+#' \lifecycle{maturing}
+#'
+#' @description add_line() from a `InputHeatmap` object, adds a line annotation layer.
+#'
+#' @importFrom rlang enquo
+#' @importFrom magrittr "%>%"
+#' @importFrom grid unit 
+#' 
+#'
+#' @name add_line
+#' @rdname add_line-method
+#'
+#' @param .data A `tbl_df` formatted as | <ELEMENT> | <FEATURE> | <VALUE> | <...> |
+#' @param .column Vector of quotes
+#' @param palette A character vector of colors, or a function such as colorRamp2 (see examples).
+#' @param size A grid::unit object, e.g. unit(2, "cm"). This is the height or width of the annotation depending on the orientation.
+#' @param ... The arguments that will be passed to top_annotation or left_annotation of the ComplexHeatmap container
+#'
+#' @details It uses `ComplexHeatmap` as visualisation tool.
+#' 
+#' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap`
+#'
+#'
+#'
+#' @examples
+#'
+#' print("DEPRECATED") 
+#'
+#'
+#' @export
+setGeneric("add_line", function(.data,
+																.column,
+																palette = NULL,size = NULL, ...)
+	standardGeneric("add_line"))
+
+#' DEPRECATED. add_line
+#' 
+#' @docType methods
+#' @rdname add_line-method
+#' 
+#'
+#' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap`
+#'
+setMethod("add_line", "InputHeatmap", function(.data,
+																							 .column,
+																							 palette = NULL, size = NULL,...){
+
+	.column = enquo(.column)
+
+	deprecate_warn("1.9.0", "tidyHeatmap::add_line()", details = "Please use `annotation_line()` instead")
+
+	annotation_line(.data = .data, .column = !!.column, palette = palette, size = size, ...)
+
+})
+
+#' DEPRECATED. Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`
+#'
+#' \lifecycle{maturing}
+#'
+#' @description add_bar() from a `InputHeatmap` object, adds a bar annotation layer.
+#'
+#' @importFrom rlang enquo
+#' @importFrom magrittr "%>%"
+#' @importFrom grid unit 
+#' 
+#'
+#' @name add_bar
+#' @rdname add_bar-method
+#'
+#' @param .data A `tbl_df` formatted as | <ELEMENT> | <FEATURE> | <VALUE> | <...> |
+#' @param .column Vector of quotes
+#' @param palette A character vector of colors, or a function such as colorRamp2 (see examples).
+#' @param size A grid::unit object, e.g. unit(2, "cm"). This is the height or width of the annotation depending on the orientation.
+#' @param ... The arguments that will be passed to top_annotation or left_annotation of the ComplexHeatmap container
+#'
+#' @details It uses `ComplexHeatmap` as visualisation tool.
+#' 
+#' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap`
+#'
+#'
+#'
+#' @examples
+#'
+#' print("DEPRECATED") 
+#'
+#'
+#' @export
+setGeneric("add_bar", function(.data,
+																			.column,
+																			palette = NULL, size = NULL,...)
+	standardGeneric("add_bar"))
+
+#' DEPRECATED. add_bar
+#' 
+#' @docType methods
+#' @rdname add_bar-method
+#' 
+#' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap`
+#'
+setMethod("add_bar", "InputHeatmap", function(.data,
+																							.column,
+																							palette = NULL, size = NULL,...){
+
+	deprecate_warn("1.9.0", "tidyHeatmap::add_bar()", details = "Please use `annotation_bar()` instead")
+
+	.column = enquo(.column)
+
+	annotation_bar(.data = .data, .column = !!.column, palette = palette, size = size, ...)
+
+})