From b5b6cc218b3fb19f631bd425f90b34f5733f709f Mon Sep 17 00:00:00 2001 From: Mengyuan Shen Date: Wed, 12 Jun 2024 13:36:35 +1000 Subject: [PATCH] reference for exported func --- DESCRIPTION | 4 +- R/data.R | 12 ++++- R/deprecated_framework.R | 16 ++++++ R/functions.R | 22 ++++---- R/methods.R | 89 ++++++++++++++++++++++++++++----- R/patchwork.R | 5 +- R/utilities.R | 4 ++ man/N52.Rd | 8 +++ man/add_annotation.Rd | 8 +++ man/add_bar-method.Rd | 8 +++ man/add_line-method.Rd | 8 +++ man/add_point-method.Rd | 8 +++ man/add_tile-method.Rd | 8 +++ man/annotation_bar-method.Rd | 8 +++ man/annotation_line-method.Rd | 8 +++ man/annotation_point-method.Rd | 8 +++ man/annotation_tile-method.Rd | 8 +++ man/as_ComplexHeatmap-method.Rd | 14 ++++++ man/heatmap-method.Rd | 8 +++ man/input_heatmap.Rd | 8 +++ man/layer_arrow_down-method.Rd | 8 +++ man/layer_arrow_up-method.Rd | 8 +++ man/layer_asterisk-method.Rd | 8 +++ man/layer_diamond-method.Rd | 8 +++ man/layer_point-method.Rd | 8 +++ man/layer_square-method.Rd | 8 +++ man/layer_star-method.Rd | 8 +++ man/layer_text-method.Rd | 8 +++ man/pasilla.Rd | 8 +++ man/save_pdf-methods.Rd | 8 +++ man/scale_robust.Rd | 8 +++ man/split-methods.Rd | 14 ++++++ man/wrap_heatmap-method.Rd | 9 +++- 33 files changed, 344 insertions(+), 29 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 01dbf97..61b8d17 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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", @@ -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 index f773c5b..776efe9 100644 --- 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" \ No newline at end of file diff --git a/R/deprecated_framework.R b/R/deprecated_framework.R index c4bb7e1..9993cc2 100644 --- 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 index 93cf8dd..3ef7d82 100644 --- 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", diff --git a/R/methods.R b/R/methods.R index e9cac27..7689c9e 100644 --- a/R/methods.R +++ b/R/methods.R @@ -78,7 +78,10 @@ InputHeatmap<-setClass( #' @rdname as_ComplexHeatmap-method #' #' @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("as_ComplexHeatmap", function(tidyHeatmap) standardGeneric("as_ComplexHeatmap")) @@ -91,7 +94,10 @@ setGeneric("as_ComplexHeatmap", function(tidyHeatmap) standardGeneric("as_Comple #' @rdname as_ComplexHeatmap-method #' #' @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) setMethod("as_ComplexHeatmap", "InputHeatmap", function(tidyHeatmap){ # Fix CRAN notes @@ -178,6 +184,10 @@ setMethod("show", "InputHeatmap", function(object){ #' @rdname plot_arithmetic #' @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) "+.InputHeatmap" <- function(e1, e2) { as_ComplexHeatmap(e1) + as_ComplexHeatmap(e2) @@ -231,6 +241,10 @@ setMethod("show", "InputHeatmap", function(object){ #' @rdname heatmap-method #' #' @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("heatmap", function(.data, .row, .column, @@ -402,6 +416,10 @@ setMethod("heatmap", "tbl_df", heatmap_) #' ) #' #' @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("annotation_tile", function(.data, .column, palette = NULL, size = NULL, ...) @@ -486,6 +504,10 @@ setMethod("annotation_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("annotation_point", function(.data, .column, palette = NULL, size = NULL,...) @@ -548,6 +570,10 @@ setMethod("annotation_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("annotation_line", function(.data, .column, palette = NULL,size = NULL, ...) @@ -611,6 +637,10 @@ setMethod("annotation_line", "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("annotation_bar", function(.data, .column, palette = NULL, size = NULL,...) @@ -672,6 +702,10 @@ setMethod("annotation_bar", "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("layer_arrow_up", function(.data,..., .size = NULL) standardGeneric("layer_arrow_up")) @@ -726,6 +760,10 @@ setMethod("layer_arrow_up", "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("layer_arrow_down", function(.data,..., .size = NULL) standardGeneric("layer_arrow_down")) @@ -779,6 +817,10 @@ setMethod("layer_arrow_down", "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("layer_point", function(.data,..., .size = NULL) standardGeneric("layer_point")) @@ -832,6 +874,10 @@ setMethod("layer_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("layer_square", function(.data,..., .size = NULL) standardGeneric("layer_square")) @@ -884,6 +930,10 @@ setMethod("layer_square", "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("layer_diamond", function(.data,..., .size = NULL) standardGeneric("layer_diamond")) @@ -895,7 +945,6 @@ setGeneric("layer_diamond", function(.data,..., #' #' #' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` -#' setMethod("layer_diamond", "InputHeatmap", function(.data,..., .size = NULL){ .data |> layer_symbol(..., symbol="diamond", .size = !!enquo(.size)) }) @@ -937,6 +986,10 @@ setMethod("layer_diamond", "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("layer_star", function(.data,..., .size = NULL) standardGeneric("layer_star")) @@ -948,7 +1001,6 @@ setGeneric("layer_star", function(.data,..., #' #' #' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` -#' setMethod("layer_star", "InputHeatmap", function(.data,..., .size = NULL){ .data |> layer_symbol(..., symbol="star", .size = !!enquo(.size)) }) @@ -990,6 +1042,10 @@ setMethod("layer_star", "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("layer_asterisk", function(.data,..., .size = NULL) standardGeneric("layer_asterisk")) @@ -1001,7 +1057,6 @@ setGeneric("layer_asterisk", function(.data,..., #' #' #' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` -#' setMethod("layer_asterisk", "InputHeatmap", function(.data,..., .size = NULL){ .data |> layer_symbol(..., symbol="asterisk", .size = !!enquo(.size)) }) @@ -1049,6 +1104,10 @@ setMethod("layer_asterisk", "InputHeatmap", function(.data,..., #' hm |> layer_text(.value = my_text) #' #' @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("layer_text", function(.data, ..., .value, @@ -1064,7 +1123,6 @@ setGeneric("layer_text", function(.data, #' #' #' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` -#' setMethod("layer_text", "InputHeatmap", function(.data, ..., .value, @@ -1156,6 +1214,10 @@ setMethod("layer_text", "InputHeatmap", function(.data, #' hm |> split_rows(2) #' #' @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("split_rows", function(.data, number_of_groups) standardGeneric("split_rows")) @@ -1168,7 +1230,6 @@ setGeneric("split_rows", function(.data, #' #' #' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` -#' setMethod("split_rows", "InputHeatmap", function(.data, number_of_groups){ @@ -1233,6 +1294,10 @@ setMethod("split_rows", "InputHeatmap", function(.data, #' hm |> split_columns(2) #' #' @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("split_columns", function(.data, number_of_groups) standardGeneric("split_columns")) @@ -1244,7 +1309,6 @@ setGeneric("split_columns", function(.data, #' #' #' @return A `InputHeatmap` object that gets evaluated to a `ComplexHeatmap` -#' setMethod("split_columns", "InputHeatmap", function(.data, number_of_groups){ @@ -1310,7 +1374,10 @@ setMethod("split_columns", "InputHeatmap", function(.data, #' @docType methods #' @rdname save_pdf-methods #' @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("save_pdf", function(.heatmap, filename, width = NULL, @@ -1351,8 +1418,6 @@ setGeneric("save_pdf", function(.heatmap, #' @param width A `double`. Plot width #' @param height A `double`. Plot height #' @param units A character string. units ("in", "cm", or "mm") -#' -#' setMethod("save_pdf", "Heatmap", .save_pdf) #' save_pdf @@ -1362,8 +1427,6 @@ setMethod("save_pdf", "Heatmap", .save_pdf) #' @param width A `double`. Plot width #' @param height A `double`. Plot height #' @param units A character string. units ("in", "cm", or "mm") -#' -#' setMethod("save_pdf", "InputHeatmap", .save_pdf) diff --git a/R/patchwork.R b/R/patchwork.R index 0688757..307f2c0 100644 --- a/R/patchwork.R +++ b/R/patchwork.R @@ -41,7 +41,10 @@ #' .value = `read count normalised log`, #' ) |> #' wrap_heatmap() -#' +#' @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( "wrap_heatmap", function(panel = NULL, plot = NULL, full = NULL, clip = TRUE, ignore_tag = FALSE, padding = NULL) standardGeneric("wrap_heatmap") diff --git a/R/utilities.R b/R/utilities.R index c2e3d28..d0f34d8 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -1066,6 +1066,10 @@ list_drop_null = function(.data){ #' @return A scaled and centred numerical array #' #' @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) scale_robust = function(y){ do_consider_df = !is.na(sd(y, na.rm=T)) && as.logical(sd(y, na.rm=T) ) diff --git a/man/N52.Rd b/man/N52.Rd index 3f2cada..118bb85 100644 --- a/man/N52.Rd +++ b/man/N52.Rd @@ -7,10 +7,18 @@ \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 520 rows and 15 columns. } +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ N52 } \description{ Example data set N52 } +\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. +} \keyword{datasets} diff --git a/man/add_annotation.Rd b/man/add_annotation.Rd index d75fc71..bb5e2c7 100644 --- a/man/add_annotation.Rd +++ b/man/add_annotation.Rd @@ -3,6 +3,9 @@ \name{add_annotation} \alias{add_annotation} \title{add_annotation} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ add_annotation( my_input_heatmap, @@ -38,3 +41,8 @@ add_annotation() takes a tbl object and easily produces a ComplexHeatmap plot, w \details{ To be added. } +\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. +} diff --git a/man/add_bar-method.Rd b/man/add_bar-method.Rd index e6fd447..8d8683f 100644 --- a/man/add_bar-method.Rd +++ b/man/add_bar-method.Rd @@ -5,6 +5,9 @@ \alias{add_bar} \alias{add_bar,InputHeatmap-method} \title{DEPRECATED. Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ add_bar(.data, .column, palette = NULL, size = NULL, ...) @@ -54,3 +57,8 @@ print("DEPRECATED") } +\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. +} diff --git a/man/add_line-method.Rd b/man/add_line-method.Rd index 21041ef..b44fe12 100644 --- a/man/add_line-method.Rd +++ b/man/add_line-method.Rd @@ -5,6 +5,9 @@ \alias{add_line} \alias{add_line,InputHeatmap-method} \title{DEPRECATED. Adds a line annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ add_line(.data, .column, palette = NULL, size = NULL, ...) @@ -40,3 +43,8 @@ print("DEPRECATED") } +\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. +} diff --git a/man/add_point-method.Rd b/man/add_point-method.Rd index 7fd2abf..dbd3a48 100644 --- a/man/add_point-method.Rd +++ b/man/add_point-method.Rd @@ -5,6 +5,9 @@ \alias{add_point} \alias{add_point,InputHeatmap-method} \title{DEPRECATED. Adds a point annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ add_point(.data, .column, palette = NULL, size = NULL, ...) @@ -40,3 +43,8 @@ print("DEPRECATED") } +\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. +} diff --git a/man/add_tile-method.Rd b/man/add_tile-method.Rd index 9f6747d..497099c 100644 --- a/man/add_tile-method.Rd +++ b/man/add_tile-method.Rd @@ -5,6 +5,9 @@ \alias{add_tile} \alias{add_tile,InputHeatmap-method} \title{DEPRECATED. Adds a tile annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ add_tile(.data, .column, palette = NULL, size = NULL, ...) @@ -39,3 +42,8 @@ It uses `ComplexHeatmap` as visualisation tool. print("DEPRECATED") } +\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. +} diff --git a/man/annotation_bar-method.Rd b/man/annotation_bar-method.Rd index e1eea99..4e090f1 100644 --- a/man/annotation_bar-method.Rd +++ b/man/annotation_bar-method.Rd @@ -5,6 +5,9 @@ \alias{annotation_bar} \alias{annotation_bar,InputHeatmap-method} \title{Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ annotation_bar(.data, .column, palette = NULL, size = NULL, ...) @@ -49,3 +52,8 @@ hm |> annotation_bar(inflection) } +\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. +} diff --git a/man/annotation_line-method.Rd b/man/annotation_line-method.Rd index 4920c96..40ccf80 100644 --- a/man/annotation_line-method.Rd +++ b/man/annotation_line-method.Rd @@ -5,6 +5,9 @@ \alias{annotation_line} \alias{annotation_line,InputHeatmap-method} \title{Adds a line annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ annotation_line(.data, .column, palette = NULL, size = NULL, ...) @@ -49,3 +52,8 @@ hm |> annotation_line(inflection) } +\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. +} diff --git a/man/annotation_point-method.Rd b/man/annotation_point-method.Rd index b150da7..815944d 100644 --- a/man/annotation_point-method.Rd +++ b/man/annotation_point-method.Rd @@ -5,6 +5,9 @@ \alias{annotation_point} \alias{annotation_point,InputHeatmap-method} \title{Adds a point annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ annotation_point(.data, .column, palette = NULL, size = NULL, ...) @@ -49,3 +52,8 @@ hm |> annotation_point(inflection) } +\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. +} diff --git a/man/annotation_tile-method.Rd b/man/annotation_tile-method.Rd index e3509cc..6d4438b 100644 --- a/man/annotation_tile-method.Rd +++ b/man/annotation_tile-method.Rd @@ -5,6 +5,9 @@ \alias{annotation_tile} \alias{annotation_tile,InputHeatmap-method} \title{Adds a tile annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ annotation_tile(.data, .column, palette = NULL, size = NULL, ...) @@ -55,3 +58,8 @@ hm |> ) } +\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. +} diff --git a/man/as_ComplexHeatmap-method.Rd b/man/as_ComplexHeatmap-method.Rd index c58158b..150bfb4 100644 --- a/man/as_ComplexHeatmap-method.Rd +++ b/man/as_ComplexHeatmap-method.Rd @@ -5,6 +5,11 @@ \alias{as_ComplexHeatmap} \alias{as_ComplexHeatmap,InputHeatmap-method} \title{Creates a `ComplexHeatmap` object for less standard plot manipulation (e.g. changing legend position)} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) + +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ as_ComplexHeatmap(tidyHeatmap) @@ -34,3 +39,12 @@ tidyHeatmap::heatmap( as_ComplexHeatmap() } +\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. + +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. +} diff --git a/man/heatmap-method.Rd b/man/heatmap-method.Rd index fd64e3b..1b97483 100644 --- a/man/heatmap-method.Rd +++ b/man/heatmap-method.Rd @@ -7,6 +7,9 @@ \alias{heatmap,tbl-method} \alias{heatmap,tbl_df-method} \title{Creates a `InputHeatmap` object from `tbl_df` on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ heatmap( .data, @@ -110,3 +113,8 @@ tidyHeatmap::N52 |> ) } +\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. +} diff --git a/man/input_heatmap.Rd b/man/input_heatmap.Rd index 991d98d..e9621a3 100644 --- a/man/input_heatmap.Rd +++ b/man/input_heatmap.Rd @@ -3,6 +3,9 @@ \name{input_heatmap} \alias{input_heatmap} \title{input_heatmap} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ input_heatmap( .data, @@ -44,3 +47,8 @@ input_heatmap() takes a tbl object and easily produces a ComplexHeatmap plot, wi \details{ To be added. } +\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. +} diff --git a/man/layer_arrow_down-method.Rd b/man/layer_arrow_down-method.Rd index ee18a99..084e82b 100644 --- a/man/layer_arrow_down-method.Rd +++ b/man/layer_arrow_down-method.Rd @@ -5,6 +5,9 @@ \alias{layer_arrow_down} \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`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ layer_arrow_down(.data, ..., .size = NULL) @@ -45,3 +48,8 @@ hm |> layer_arrow_down() } +\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. +} diff --git a/man/layer_arrow_up-method.Rd b/man/layer_arrow_up-method.Rd index 4e776f9..0e7c602 100644 --- a/man/layer_arrow_up-method.Rd +++ b/man/layer_arrow_up-method.Rd @@ -5,6 +5,9 @@ \alias{layer_arrow_up} \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`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ layer_arrow_up(.data, ..., .size = NULL) @@ -45,3 +48,8 @@ hm |> layer_arrow_up() } +\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. +} diff --git a/man/layer_asterisk-method.Rd b/man/layer_asterisk-method.Rd index ca9df52..4f4f3cc 100644 --- a/man/layer_asterisk-method.Rd +++ b/man/layer_asterisk-method.Rd @@ -5,6 +5,9 @@ \alias{layer_asterisk} \alias{layer_asterisk,InputHeatmap-method} \title{Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ layer_asterisk(.data, ..., .size = NULL) @@ -45,3 +48,8 @@ hm |> layer_asterisk() } +\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. +} diff --git a/man/layer_diamond-method.Rd b/man/layer_diamond-method.Rd index 819b924..8627c88 100644 --- a/man/layer_diamond-method.Rd +++ b/man/layer_diamond-method.Rd @@ -5,6 +5,9 @@ \alias{layer_diamond} \alias{layer_diamond,InputHeatmap-method} \title{Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ layer_diamond(.data, ..., .size = NULL) @@ -45,3 +48,8 @@ hm |> layer_diamond() } +\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. +} diff --git a/man/layer_point-method.Rd b/man/layer_point-method.Rd index f5dc615..facc6d1 100644 --- a/man/layer_point-method.Rd +++ b/man/layer_point-method.Rd @@ -5,6 +5,9 @@ \alias{layer_point} \alias{layer_point,InputHeatmap-method} \title{Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ layer_point(.data, ..., .size = NULL) @@ -45,3 +48,8 @@ hm |> layer_point() } +\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. +} diff --git a/man/layer_square-method.Rd b/man/layer_square-method.Rd index 96577d4..d9d6e00 100644 --- a/man/layer_square-method.Rd +++ b/man/layer_square-method.Rd @@ -5,6 +5,9 @@ \alias{layer_square} \alias{layer_square,InputHeatmap-method} \title{Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ layer_square(.data, ..., .size = NULL) @@ -45,3 +48,8 @@ hm |> layer_square() } +\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. +} diff --git a/man/layer_star-method.Rd b/man/layer_star-method.Rd index 7399a10..0c78bdf 100644 --- a/man/layer_star-method.Rd +++ b/man/layer_star-method.Rd @@ -5,6 +5,9 @@ \alias{layer_star} \alias{layer_star,InputHeatmap-method} \title{Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ layer_star(.data, ..., .size = NULL) @@ -45,3 +48,8 @@ hm |> layer_star() } +\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. +} diff --git a/man/layer_text-method.Rd b/man/layer_text-method.Rd index 8132036..df5c185 100644 --- a/man/layer_text-method.Rd +++ b/man/layer_text-method.Rd @@ -5,6 +5,9 @@ \alias{layer_text} \alias{layer_text,InputHeatmap-method} \title{Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ layer_text(.data, ..., .value, .size = NULL) @@ -49,3 +52,8 @@ hm |> layer_text(.value = "a") hm |> layer_text(.value = my_text) } +\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. +} diff --git a/man/pasilla.Rd b/man/pasilla.Rd index 1ac8548..536569b 100644 --- a/man/pasilla.Rd +++ b/man/pasilla.Rd @@ -7,10 +7,18 @@ \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 504 rows and 8 columns. } +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ pasilla } \description{ Example data set Pasilla } +\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. +} \keyword{datasets} diff --git a/man/save_pdf-methods.Rd b/man/save_pdf-methods.Rd index cd2345d..54f06fc 100644 --- a/man/save_pdf-methods.Rd +++ b/man/save_pdf-methods.Rd @@ -4,6 +4,9 @@ \name{save_pdf} \alias{save_pdf} \title{Save plot on PDF file} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ save_pdf( .heatmap, @@ -48,3 +51,8 @@ It simply save an `Heatmap` to a PDF file use pdf() function in the back end } +\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. +} diff --git a/man/scale_robust.Rd b/man/scale_robust.Rd index aeecb11..c3e92ca 100644 --- a/man/scale_robust.Rd +++ b/man/scale_robust.Rd @@ -3,6 +3,9 @@ \name{scale_robust} \alias{scale_robust} \title{Scale counts in a robust way against sd == 0} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ scale_robust(y) } @@ -15,3 +18,8 @@ A scaled and centred numerical array \description{ Scale counts in a robust way against sd == 0 } +\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. +} diff --git a/man/split-methods.Rd b/man/split-methods.Rd index da612ec..986bc19 100644 --- a/man/split-methods.Rd +++ b/man/split-methods.Rd @@ -7,6 +7,11 @@ \alias{split_columns} \alias{split_columns,InputHeatmap-method} \title{Split the heatmap row-wise depending on the biggest branches in the cladogram.} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) + +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ split_rows(.data, number_of_groups) @@ -70,3 +75,12 @@ hm = hm |> split_columns(2) } +\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. + +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. +} diff --git a/man/wrap_heatmap-method.Rd b/man/wrap_heatmap-method.Rd index b11425a..b2bddbf 100644 --- a/man/wrap_heatmap-method.Rd +++ b/man/wrap_heatmap-method.Rd @@ -5,6 +5,9 @@ \alias{wrap_heatmap} \alias{wrap_heatmap,InputHeatmap-method} \title{Wrap tidyHeatmap (ComplexHeatmap) in a patchwork-compliant patch} +\source{ +[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472) +} \usage{ wrap_heatmap( panel = NULL, @@ -60,5 +63,9 @@ tidyHeatmap::heatmap( .value = `read count normalised log`, ) |> wrap_heatmap() - +} +\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. }