Feature/jgqo373 watermark decorator

.gitignore

@@ -1,2 +1,4 @@
 *.Rcheck
 *.tar.gz
+*.Rproj
+.Rproj.user

DESCRIPTION

@@ -50,6 +50,7 @@ Imports:
   teal.code,
   tern,
   yaml,
+  gridify,
   teal.modules.clinical
 Suggests:
   forcats,

NAMESPACE

@@ -11,29 +11,89 @@ export(or_filtering_transformator)
 export(patchwork_plot_decorator)
 export(remove_by_label)
 export(title_footer_decorator)
-import(R6)
-import(checkmate)
-import(dplyr)
-import(ggplot2)
-import(ggplotify)
-import(openxlsx)
-import(patchwork)
-import(rlang)
-import(rtables)
+export(watermark_decorator)
 import(shiny)
-import(shinyBS)
-import(shinyWidgets)
 import(teal)
-import(tern)
-import(yaml)
+importFrom(R6,R6Class)
+importFrom(checkmate,assert_character)
+importFrom(checkmate,assert_class)
+importFrom(checkmate,assert_multi_class)
+importFrom(checkmate,assert_number)
+importFrom(checkmate,assert_true)
+importFrom(cowplot,as_grob)
 importFrom(cowplot,plot_grid)
+importFrom(dplyr,filter)
+importFrom(ggplot2,.pt)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,annotate)
+importFrom(ggplot2,arrow)
+importFrom(ggplot2,coord_cartesian)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_line)
+importFrom(ggplot2,element_rect)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_text)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,layer_scales)
+importFrom(ggplot2,margin)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_x_discrete)
+importFrom(ggplot2,scale_y_continuous)
+importFrom(ggplot2,scale_y_discrete)
+importFrom(ggplot2,theme)
+importFrom(ggplotify,as.ggplot)
 importFrom(grDevices,graphics.off)
+importFrom(grid,unit)
+importFrom(gridify,gridify)
+importFrom(gridify,gridifyCell)
+importFrom(gridify,gridifyCells)
+importFrom(gridify,gridifyLayout)
+importFrom(gridify,gridifyObject)
+importFrom(gridify,set_cell)
 importFrom(methods,new)
+importFrom(openxlsx,read.xlsx)
+importFrom(patchwork,plot_annotation)
 importFrom(rlang,parse_expr)
+importFrom(rtables,as_result_df)
+importFrom(shiny,NS)
+importFrom(shiny,actionButton)
+importFrom(shiny,checkboxInput)
+importFrom(shiny,div)
+importFrom(shiny,eventReactive)
+importFrom(shiny,hr)
+importFrom(shiny,insertUI)
+importFrom(shiny,modalDialog)
+importFrom(shiny,moduleServer)
+importFrom(shiny,observe)
+importFrom(shiny,observeEvent)
+importFrom(shiny,reactive)
+importFrom(shiny,reactiveVal)
+importFrom(shiny,reactiveValues)
+importFrom(shiny,renderText)
+importFrom(shiny,renderUI)
+importFrom(shiny,req)
+importFrom(shiny,selectInput)
+importFrom(shiny,showModal)
+importFrom(shiny,showNotification)
+importFrom(shiny,span)
+importFrom(shiny,tagAppendChild)
+importFrom(shiny,tagList)
+importFrom(shiny,tags)
+importFrom(shiny,textInput)
+importFrom(shiny,uiOutput)
+importFrom(shiny,updateSelectInput)
+importFrom(shinyBS,bsModal)
+importFrom(shinyWidgets,pickerInput)
 importFrom(shinyjs,hidden)
 importFrom(shinyjs,hide)
 importFrom(shinyjs,show)
 importFrom(shinyjs,toggle)
+importFrom(shinyjs,useShinyjs)
+importFrom(teal,teal_transform_module)
 importFrom(teal.code,eval_code)
 importFrom(teal.modules.clinical,add_expr)
 importFrom(teal.modules.clinical,bracket_expr)
+importFrom(tern,rtable2gg)
+importFrom(yaml,as.yaml)

NEWS.md

@@ -1,6 +1,7 @@
 # Version 0.0.2.9000
 
 - Refactored the `merge_levels_transformator` to handle the predefined inputs to the transformator.
+- Added new `watermark_decorator`([#23](https://github.com/phuse-org/uteals/pull/23)).
 
 # Version 0.0.2
 

R/create_rel_risk_transformator.R

@@ -12,7 +12,8 @@
 #' @param control_group (`character(1)`) one of the existing level from the selected `column_name`.
 #' @param label_name (`character(1)`) label for the new field or variable.
 #'
-#' @import teal shiny
+#' @importFrom teal teal_transform_module
+#' @importFrom shiny NS tagList selectInput textInput moduleServer observe updateSelectInput reactive
 #'
 #' @return `teal::teal_transform_module`
 #'

R/forest_plot_decorator.R

@@ -170,7 +170,12 @@ forestplot_x_decorator <- function() {
 #'   printed side-by-side via [cowplot::plot_grid()].
 #'
 #' @return `ggplot` forest plot and table.
-#' @import checkmate tern ggplot2 rtables
+#' @importFrom checkmate assert_class assert_number assert_character assert_true
+#' @importFrom tern rtable2gg
+#' @importFrom ggplot2 ggplot theme scale_x_continuous scale_y_continuous coord_cartesian annotate geom_point margin
+#' @importFrom ggplot2 element_rect element_blank element_line element_text aes arrow .pt
+#' @importFrom rtables as_result_df
+#' @importFrom grid unit
 #' @importFrom cowplot plot_grid
 #'
 #' @export

R/ggplot_decorator.R

@@ -31,7 +31,10 @@
 #' of `ggplot` options given in the `plot_options` parameter value.
 #' The entered `ggplot` options are applied to `ggplot` plot object.
 #'
-#' @import teal shiny ggplot2
+#' @importFrom teal teal_transform_module
+#' @importFrom shiny NS tagList tagAppendChild textInput moduleServer reactive req
+#' @importFrom ggplot2 labs theme element_text scale_y_continuous scale_x_continuous scale_x_discrete
+#' @importFrom ggplot2 scale_y_discrete geom_text layer_scales
 #'
 #' @examples
 #' app <- teal::init(
@@ -195,7 +198,7 @@ ggplot_decorator <- function(output_name,
                   output_name <- output_name +
                     ggplot2::scale_y_continuous(
                       breaks = layer_scales(output_name)$y$break_positions(),
-                      labels = trimws(str_split(y_labels_cont, ",")[[1]])
+                      labels = trimws(strsplit(y_labels_cont, ",")[[1]])
                     )
                 },
                 output_name = as.name(output_name),
@@ -212,7 +215,7 @@ ggplot_decorator <- function(output_name,
                 data4,
                 {
                   output_name <- output_name +
-                    ggplot2::scale_x_continuous(breaks = trimws(str_split(x_breaks, ",")[[1]]))
+                    ggplot2::scale_x_continuous(breaks = trimws(strsplit(x_breaks, ",")[[1]]))
                 },
                 output_name = as.name(output_name),
                 x_breaks = input$x_breaks
@@ -229,7 +232,7 @@ ggplot_decorator <- function(output_name,
                   output_name <- output_name +
                     ggplot2::scale_x_continuous(
                       breaks = layer_scales(output_name)$x$break_positions(),
-                      labels = trimws(str_split(x_labels_cont, ",")[[1]])
+                      labels = trimws(strsplit(x_labels_cont, ",")[[1]])
                     )
                 },
                 output_name = as.name(output_name),
@@ -245,7 +248,7 @@ ggplot_decorator <- function(output_name,
               data7 <- within(
                 data6,
                 {
-                  x_labels_discrete <- trimws(str_split(x_labels_discrete, ",")[[1]])
+                  x_labels_discrete <- trimws(strsplit(x_labels_discrete, ",")[[1]])
                   output_name <- output_name + ggplot2::scale_x_discrete(labels = x_labels_discrete)
                 },
                 output_name = as.name(output_name),
@@ -261,7 +264,7 @@ ggplot_decorator <- function(output_name,
               data8 <- within(
                 data7,
                 {
-                  y_labels_discrete <- trimws(str_split(y_labels_discrete, ",")[[1]])
+                  y_labels_discrete <- trimws(strsplit(y_labels_discrete, ",")[[1]])
                   output_name <- output_name + ggplot2::scale_y_discrete(labels = y_labels_discrete)
                 },
                 output_name = as.name(output_name),

R/merge_levels_transformator.R

@@ -1,5 +1,6 @@
-##' R6 Class for managing the transformation objects
-TransformationManager <- R6::R6Class(
+# TransformationManager R6 Class for managing the transformation objects
+# @noRd
+TransformationManager <- R6::R6Class( # nolint: object_name_linter.
   "TransformationManager",
   public = list(
     counter = 0,
@@ -13,7 +14,7 @@ TransformationManager <- R6::R6Class(
     add_id = function() {
       self$counter <- self$counter + 1
       self$active_ids(c(self$active_ids(), self$counter))
-      return(self$counter)
+      self$counter
     },
     remove_id = function(id) {
       self$active_ids(setdiff(self$active_ids(), id))
@@ -27,10 +28,13 @@ TransformationManager <- R6::R6Class(
 )
 
 #' UI design of the transformator
+#'
+#' @param id (`character(1)`) the id of the module.
+#' @noRd
 merge_level_transformer_ui <- function(id) {
   ns <- NS(id)
   tagList(
-    useShinyjs(),
+    shinyjs::useShinyjs(),
     tags$div(id = ns("transformation_container")),
     hr(),
     actionButton(ns("add"), "Add", class = "btn-primary"),
@@ -55,7 +59,10 @@ merge_level_transformer_srv <- function(id, data, manager, dataname) {
         req(input[[paste0("col_name_", idx)]])
         col_data <- data()[[dataname]][[input[[paste0("col_name_", idx)]]]]
         choices <- if (is.factor(col_data)) levels(col_data) else unique(col_data)
-        selectInput(ns(paste0("levs_", idx)), "Levels to Update", choices = choices, multiple = TRUE, selected = lev_sel)
+        selectInput(
+          ns(paste0("levs_", idx)), "Levels to Update",
+          choices = choices, multiple = TRUE, selected = lev_sel
+        )
       })
     }
 
@@ -82,7 +89,10 @@ merge_level_transformer_srv <- function(id, data, manager, dataname) {
           div(
             id = body_id,
             style = "margin-top: 10px;",
-            selectInput(ns(paste0("col_name_", idx)), "Variable", choices = names(data()[[dataname]]), selected = var_sel),
+            selectInput(
+              ns(paste0("col_name_", idx)), "Variable",
+              choices = names(data()[[dataname]]), selected = var_sel
+            ),
             uiOutput(ns(paste0("col_levels_ui_", idx))),
             textInput(ns(paste0("new_label_", idx)), "New Level Name", value = new_name)
           ),
@@ -189,7 +199,10 @@ merge_level_transformer_srv <- function(id, data, manager, dataname) {
 #' which columns will be used for possible transformation.
 #' @param predefined (`list`) the list which has variable name, levels and new label
 #'
-#' @import teal shiny shinyWidgets
+#' @importFrom teal teal_transform_module
+#' @importFrom shiny NS tagList actionButton hr div tags uiOutput renderUI req
+#' @importFrom shiny selectInput textInput moduleServer reactiveVal observeEvent observe eventReactive reactive
+#' @importFrom shinyWidgets pickerInput
 #' @importFrom teal.code eval_code
 #' @importFrom teal.modules.clinical add_expr bracket_expr
 #'

R/or_filtering_transformator.R

@@ -41,10 +41,15 @@
 #'
 #' @param dataname (`character(1)`) Name of the dataset to filter. Pass a single dataset name as a string.
 #'
-#' @import teal shiny shinyWidgets dplyr shinyBS rlang
-#' @importFrom methods new
-#' @importFrom shinyjs toggle show hidden hide
+#' @importFrom teal teal_transform_module
+#' @importFrom shiny NS tagList renderText renderUI div span actionButton observeEvent insertUI
+#' @importFrom shiny updateSelectInput showNotification showModal modalDialog reactiveValues observe reactive
+#' @importFrom shinyWidgets pickerInput
+#' @importFrom dplyr filter
+#' @importFrom shinyBS bsModal
 #' @importFrom rlang parse_expr
+#' @importFrom methods new
+#' @importFrom shinyjs toggle show hidden hide useShinyjs
 #'
 #' @return `teal::teal_transform_module`
 #'

R/or_filtering_transformator_view_model.R

@@ -1,6 +1,6 @@
 #' View model for [or_filtering_transformator()].
 #'
-#' @import R6
+#' @importFrom R6 R6Class
 #' @keywords internal
 filtering_transformator_model <- R6::R6Class("filtering_transformator_model",
   public = list(

R/patchwork_plot_decorator.R

@@ -9,7 +9,9 @@
 #' @details The module creates a UI with text controls for plot title and footnote.
 #' The entered title and footnote text are applied to the patchwork plots.
 #'
-#' @import teal shiny patchwork
+#' @importFrom teal teal_transform_module
+#' @importFrom shiny NS tagList textInput moduleServer reactive req
+#' @importFrom patchwork plot_annotation
 #'
 #' @export
 patchwork_plot_decorator <- function(output_name, label_text = "decorator") {

R/r_access_utilities.R

@@ -11,7 +11,7 @@
 #'
 #' @return Character vector of non-parent module labels
 #'
-#' @import yaml
+#' @importFrom yaml as.yaml
 #' @examples
 #' # Extract modules from mods object to YAML file
 #' mods <- teal::modules(
@@ -21,6 +21,11 @@
 #' labels <- extract_modules_to_yaml(mods, "panel_str_modules.yml")
 #' unlink("panel_str_modules.yml")
 #'
+#' # Clean up
+#' if (file.exists("panel_str_modules.yml")) {
+#'   file.remove("panel_str_modules.yml")
+#' }
+#'
 #' @export
 extract_modules_to_yaml <- function(mods, filepath, verbose = FALSE) {
   # Recursively extract module labels, excluding parent containers
@@ -58,7 +63,7 @@ extract_modules_to_yaml <- function(mods, filepath, verbose = FALSE) {
   if (verbose) {
     message("Generated ", filepath, " with ", length(non_parent_labels), " non-parent module labels")
   }
-  
+
   non_parent_labels
 }
 
@@ -74,7 +79,7 @@ extract_modules_to_yaml <- function(mods, filepath, verbose = FALSE) {
 #'
 #' @return Filtered `teal_modules` or `teal_module` object, or `NULL` if none matches.
 #'
-#' @import checkmate
+#' @importFrom checkmate assert_multi_class
 #' @examples
 #' # Keep only specific modules by label
 #' mods <- teal::modules(
@@ -113,7 +118,7 @@ keep_by_label <- function(x, label) {
 #' @return The filtered teal modules object with matching modules removed, or `NULL`
 #'   if all modules are removed.
 #'
-#' @import checkmate
+#' @importFrom checkmate assert_multi_class
 #' @examples
 #' mods <- teal::modules(
 #'   teal::example_module("mod1"),

R/title_footer_decorator.R

@@ -27,7 +27,12 @@
 #' @seealso For the exact Excel workbook layout expected by this function, see the package vignette:
 #' `vignette("title-footer-decorator-excel-structure", package = "uteals")`
 #'
-#' @import openxlsx ggplotify ggplot2 patchwork teal shiny
+#' @importFrom openxlsx read.xlsx
+#' @importFrom ggplotify as.ggplot
+#' @importFrom ggplot2 labs theme element_text
+#' @importFrom patchwork plot_annotation
+#' @importFrom teal teal_transform_module
+#' @importFrom shiny NS tagList div selectInput checkboxInput uiOutput renderUI textInput moduleServer reactive req
 #' @importFrom grDevices graphics.off
 #'
 #' @examples