Merge pull request #130 from myushen/reference

reference for exported func
stemangiola · Sep 3, 2024 · a9c5d39 · a9c5d39
2 parents 5d9409e + e050870
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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: 1.10.3
+Version: 1.10.2
 Authors@R: 
     c(person(given = "Stefano",
            family = "Mangiola",
@@ -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
diff --git a/R/data.R b/R/data.R
@@ -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"
diff --git a/R/deprecated_framework.R b/R/deprecated_framework.R
@@ -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,...)
@@ -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, ...)
@@ -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,...)
@@ -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, ...)

diff --git a/R/functions.R b/R/functions.R
@@ -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,
@@ -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))),
@@ -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",