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reference for exported func #130

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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Type: Package
Package: tidyHeatmap
Title: A Tidy Implementation of Heatmap
Version: 1.10.1
Version: 1.10.2
Authors@R:
c(person(given = "Stefano",
family = "Mangiola",
Expand Down Expand Up @@ -67,5 +67,5 @@ Biarch: true
biocViews: AssayDomain, Infrastructure
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
RoxygenNote: 7.3.1
Language: en-US
12 changes: 10 additions & 2 deletions R/data.R
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@@ -1,11 +1,19 @@
#' Example data set N52
#'
#'
#'
#' @docType data
#' @references Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
#' modular heatmap production based on tidy principles." Journal of Open Source Software.
#' doi:10.21105/joss.02472.
#' @source [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
"N52"

#' Example data set Pasilla
#'
#'
#'
#' @docType data
#' @references Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
#' modular heatmap production based on tidy principles." Journal of Open Source Software.
#' doi:10.21105/joss.02472.
#' @source [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
"pasilla"
16 changes: 16 additions & 0 deletions R/deprecated_framework.R
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Expand Up @@ -496,6 +496,10 @@ annot_to_list_OLD = function(.data){
#'
#'
#' @export
#' @references Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
#' modular heatmap production based on tidy principles." Journal of Open Source Software.
#' doi:10.21105/joss.02472.
#' @source [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
setGeneric("add_bar", function(.data,
.column,
palette = NULL, size = NULL,...)
Expand Down Expand Up @@ -531,6 +535,10 @@ setGeneric("add_bar", function(.data,
#' print("DEPRECATED")
#'
#' @export
#' @references Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
#' modular heatmap production based on tidy principles." Journal of Open Source Software.
#' doi:10.21105/joss.02472.
#' @source [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
setGeneric("add_tile", function(.data,
.column,
palette = NULL, size = NULL, ...)
Expand Down Expand Up @@ -587,6 +595,10 @@ setMethod("add_tile", "InputHeatmap", function(.data,
#'
#'
#' @export
#' @references Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
#' modular heatmap production based on tidy principles." Journal of Open Source Software.
#' doi:10.21105/joss.02472.
#' @source [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
setGeneric("add_point", function(.data,
.column,
palette = NULL, size = NULL,...)
Expand Down Expand Up @@ -643,6 +655,10 @@ setMethod("add_point", "InputHeatmap", function(.data,
#'
#'
#' @export
#' @references Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
#' modular heatmap production based on tidy principles." Journal of Open Source Software.
#' doi:10.21105/joss.02472.
#' @source [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
setGeneric("add_line", function(.data,
.column,
palette = NULL,size = NULL, ...)
Expand Down
22 changes: 12 additions & 10 deletions R/functions.R
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Expand Up @@ -42,11 +42,10 @@
#'
#' @return A `ComplexHeatmap` object
#'
#'
#'
#'
#'
#'
#' @references Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
#' modular heatmap production based on tidy principles." Journal of Open Source Software.
#' doi:10.21105/joss.02472.
#' @source [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
input_heatmap = function(.data,
.horizontal,
.vertical,
Expand Down Expand Up @@ -295,11 +294,10 @@ add_grouping = function(my_input_heatmap){
#'
#' @return A `ComplexHeatmap` object
#'
#'
#'
#'
#'
#'
#' @references Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
#' modular heatmap production based on tidy principles." Journal of Open Source Software.
#' doi:10.21105/joss.02472.
#' @source [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
add_annotation = function(my_input_heatmap,
annotation,
type = rep("tile", length(quo_names(annotation))),
Expand Down Expand Up @@ -444,6 +442,10 @@ add_annotation = function(my_input_heatmap,
#'
#' hm |> layer_symbol()
#'
#' @references Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
#' modular heatmap production based on tidy principles." Journal of Open Source Software.
#' doi:10.21105/joss.02472.
#' @source [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
setGeneric("layer_symbol", function(.data,
...,
symbol = "point",
Expand Down
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