Merge remote-tracking branch 'origin/pre-release@main' into 686-asser…

…tions_process@pre-release@main

* origin/pre-release@main:
  removed @nord tags and added return from shared_params
  missing comma
  641 non exported functions (#680)
  pre-release vignettes review (#681)
  [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
  Standardise function titles similar to what we have in tmc (#691)
  [skip actions] Bump version to 0.2.16.9026
  `tm_g_regression` labels are no longer allowed out of bounds (#675)
  [skip actions] Bump version to 0.2.16.9025
  Remove the internal function `var_labels` in favour of `teal.data::col_labels` (#690)
  [skip actions] Bump version to 0.2.16.9024
  Fix the silent error in `tm_a_pca` (#688)

.lintr

@@ -1,5 +1,6 @@
 linters: linters_with_defaults(
   line_length_linter = line_length_linter(120),
   cyclocomp_linter = NULL,
-  object_usage_linter = NULL
+  object_usage_linter = NULL,
+  object_name_linter = object_name_linter(styles = c("snake_case", "symbols"), regexes = c(ANL = "^ANL_?[0-9]*$", ADaM = "^r?AD[A-Z]{2,3}_?[0-9]*$"))
   )

.pre-commit-config.yaml

@@ -24,6 +24,7 @@ repos:
           - dplyr
           - DT
           - forcats
+          - ggrepel
           - grid
           - logger
           - scales

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.general
 Title: General Modules for 'teal' Applications
-Version: 0.2.16.9023
-Date: 2024-02-22
+Version: 0.2.16.9026
+Date: 2024-02-27
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "aut"),
@@ -59,6 +59,7 @@ Suggests:
     ggExtra,
     ggpmisc (>= 0.4.3),
     ggpp,
+    ggrepel,
     goftest,
     gridExtra,
     htmlwidgets,
@@ -84,9 +85,10 @@ Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     insightsengineering/teal.widgets, insightsengineering/tern,
     tidyverse/tibble, tidyverse/tidyr, tidymodels/broom,
     daattali/colourpicker, daattali/ggExtra, aphalo/ggpmisc, aphalo/ggpp,
-    baddstats/goftest, gridExtra, ramnathv/htmlwidgets, jeroen/jsonlite,
-    yihui/knitr, deepayan/lattice, MASS, insightsengineering/nestcolor,
-    r-lib/rlang, insightsengineering/rtables, htmlwidgets/sparkline,
+    slowkow/ggrepel, baddstats/goftest, gridExtra, ramnathv/htmlwidgets,
+    jeroen/jsonlite, yihui/knitr, deepayan/lattice, MASS,
+    insightsengineering/nestcolor, r-lib/rlang,
+    insightsengineering/rtables, sparkline, insightsengineering/teal.data,
     r-lib/testthat
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8

NEWS.md

@@ -1,9 +1,13 @@
-# teal.modules.general 0.2.16.9023
+# teal.modules.general 0.2.16.9026
 
 ### Enhancements
 
 * Updated the package docs and vignettes with the new way of specifying data for `teal::init()`. The `data` argument will accept a `teal_data` object
 
+### Bug fixes
+
+* Outlier labels no longer appear out of bounds in `tm_a_regression`.
+
 ### Miscellaneous
 
 * Removed `teal.slice` dependencies.

R/tm_a_pca.R

@@ -1,4 +1,4 @@
-#' Principal component analysis module
+#' `teal` module: Principal component analysis
 #'
 #' Module conducts principal component analysis (PCA) on a given dataset and offers different
 #' ways of visualizing the outcomes, including elbow plot, circle plot, biplot, and eigenvector plot.
@@ -9,19 +9,15 @@
 #' @inheritParams shared_params
 #' @param dat (`data_extract_spec` or `list` of multiple `data_extract_spec`)
 #'   specifying columns used to compute PCA.
-#' @param alpha (`numeric`, optional) Specifies point opacity.
-#' - If vector of `length == 1` then the plot points will have a fixed opacity.
-#' - while vector of `value`, `min`, and `max` allows dynamic adjustment.
-#' @param size (`numeric`, optional) Specifies point size.
-#' - If vector of `length == 1` then the plot point sizes will have a fixed size
-#' - while vector of `value`, `min`, and `max` allows dynamic adjustment.
 #' @param font_size (`numeric`, optional) Specifies font size.
 #' It controls the font size for plot titles, axis labels, and legends.
 #' - If vector of `length == 1` then the font sizes will have a fixed size.
 #' - while vector of `value`, `min`, and `max` allows dynamic adjustment.
 #' @templateVar ggnames "Elbow plot", "Circle plot", "Biplot", "Eigenvector plot"
 #' @template ggplot2_args_multi
 #'
+#' @inherit shared_params return
+#'
 #' @examples
 #' library(teal.widgets)
 #'
@@ -306,11 +302,10 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
       response[[i]]$select$multiple <- FALSE
       response[[i]]$select$always_selected <- NULL
       response[[i]]$select$selected <- NULL
-      response[[i]]$select$choices <- teal.data::col_labels(isolate(data())[[response[[i]]$dataname]])
-      response[[i]]$select$choices <- setdiff(
-        response[[i]]$select$choices,
-        unlist(teal.data::join_keys(isolate(data()))[[response[[i]]$dataname]])
-      )
+      all_cols <- teal.data::col_labels(isolate(data())[[response[[i]]$dataname]])
+      ignore_cols <- unlist(teal.data::join_keys(isolate(data()))[[response[[i]]$dataname]])
+      color_cols <- all_cols[!names(all_cols) %in% ignore_cols]
+      response[[i]]$select$choices <- choices_labeled(names(color_cols), color_cols)
     }
 
     selector_list <- teal.transform::data_extract_multiple_srv(

R/tm_data_table.R

@@ -1,4 +1,4 @@
-#' Data table viewer module
+#' `teal` module: Data table viewer
 #'
 #' Module provides a dynamic and interactive way to view `data.frame`s in a `teal` application.
 #' It uses the `DT` package to display data tables in a paginated, searchable, and sortable format,
@@ -27,6 +27,8 @@
 #' @param server_rendering (`logical`) should the data table be rendered server side
 #' (see `server` argument of [DT::renderDataTable()])
 #'
+#' @inherit shared_params return
+#'
 #' @examples
 #' # general data example
 #' data <- teal_data()

R/tm_file_viewer.R

@@ -1,4 +1,4 @@
-#' File viewer module
+#' `teal` module: File viewer
 #'
 #' The file viewer module provides a tool to view static files.
 #' Supported formats include text formats, `PDF`, `PNG` `APNG`,
@@ -8,18 +8,20 @@
 #' @inheritParams shared_params
 #' @param input_path (`list`) of the input paths, optional. Each element can be:
 #'
-#' 1. Specific path to files of accepted formats
-#' 2. A directory or a URL
+#' @inherit shared_params return
 #'
-#' The paths can be specified as absolute paths or relative to the running
-#' directory of the application.
+#' Paths can be specified as absolute paths or relative to the running directory of the application.
 #' Default to the current working directory if not supplied.
 #'
-#' @inherit shared_params return
-#'
 #' @examples
+#' data <- teal_data()
+#' data <- within(data, {
+#'   data <- data.frame(1)
+#' })
+#' datanames(data) <- c("data")
+#'
 #' app <- init(
-#'   data = teal_data(data = 1), # Mock dataset to initialize the app without error
+#'   data = data,
 #'   modules = modules(
 #'     tm_file_viewer(
 #'       input_path = list(
@@ -34,6 +36,7 @@
 #' if (interactive()) {
 #'   shinyApp(app$ui, app$server)
 #' }
+#'
 #' @export
 #'
 tm_file_viewer <- function(label = "File Viewer Module",

R/tm_front_page.R

@@ -1,4 +1,4 @@
-#' Front page module
+#' `teal` module: Front page
 #'
 #' Creates a simple front page for `teal` applications, displaying
 #' introductory text, tables, additional `html` or `shiny` tags, and footnotes.
@@ -15,17 +15,17 @@
 #' element, if named the name is shown first in bold, followed by the value.
 #' @param show_metadata (`logical`) indicating whether the metadata of the datasets be available on the module.
 #'
-#' @examples
+#' @inherit shared_params return
 #'
+#' @examples
 #' data <- teal_data()
 #' data <- within(data, {
 #'   require(nestcolor)
-#'   ADSL <- teal.modules.general::rADSL
+#'   ADSL <- rADSL
 #'   attr(ADSL, "metadata") <- list("Author" = "NEST team", "data_source" = "synthetic data")
 #' })
-#' datanames <- c("ADSL")
-#' datanames(data) <- datanames
-#' join_keys(data) <- default_cdisc_join_keys[datanames]
+#' datanames(data) <- "ADSL"
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
 #'
 #' table_1 <- data.frame(Info = c("A", "B"), Text = c("A", "B"))
 #' table_2 <- data.frame(`Column 1` = c("C", "D"), `Column 2` = c(5.5, 6.6), `Column 3` = c("A", "B"))
@@ -40,7 +40,7 @@
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
-#'     teal.modules.general::tm_front_page(
+#'     tm_front_page(
 #'       header_text = c(
 #'         "Important information" = "It can go here.",
 #'         "Other information" = "Can go here."

R/tm_g_association.R

@@ -1,4 +1,4 @@
-#' Stack plots of variables and show association with reference variable
+#' `teal` module: Stack plots of variables and show association with reference variable
 #'
 #' Module provides functionality for visualizing the distribution of variables and
 #' their association with a reference variable.
@@ -23,6 +23,8 @@
 #' @templateVar ggnames "Bivariate1", "Bivariate2"
 #' @template ggplot2_args_multi
 #'
+#' @inherit shared_params return
+#'
 #' @examples
 #' library(teal.widgets)
 #'

R/tm_g_bivariate.R

@@ -1,4 +1,4 @@
-#' Univariate and bivariate visualizations module
+#' `teal` module: Univariate and bivariate visualizations
 #'
 #' Module enables the creation of univariate and bivariate plots,
 #' facilitating the exploration of data distributions and relationships between two variables.
@@ -44,10 +44,12 @@
 #' Does not allow scaling to be changed by default (`FALSE`).
 #' @param swap_axes (`logical`, optional) Whether to swap X and Y axes. Defaults to `FALSE`.
 #'
+#' @inherit shared_params return
+#'
 #' @examples
 #' library(teal.widgets)
 #'
-#' # general data exapmle
+#' # general data example
 #' data <- teal_data()
 #' data <- within(data, {
 #'   require(nestcolor)
@@ -299,9 +301,7 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
   )
 }
 
-# UI function for the bivariate module.
-#' @noRd
-#' @keywords internal
+# UI function for the bivariate module
 ui_g_bivariate <- function(id, ...) {
   args <- list(...)
   is_single_dataset_value <- teal.transform::is_single_dataset(
@@ -442,9 +442,7 @@ ui_g_bivariate <- function(id, ...) {
   )
 }
 
-# Server function for the bivariate module.
-#' @noRd
-#' @keywords internal
+# Server function for the bivariate module
 srv_g_bivariate <- function(id,
                             data,
                             reporter,
@@ -726,8 +724,6 @@ srv_g_bivariate <- function(id,
 }
 
 # Get Substituted ggplot call
-#' @noRd
-#' @keywords internal
 bivariate_plot_call <- function(data_name,
                                 x = character(0),
                                 y = character(0),
@@ -778,8 +774,6 @@ bivariate_plot_call <- function(data_name,
 
 # Create ggplot part of plot call
 # Due to the type of the x and y variable the plot type is chosen
-#' @noRd
-#' @keywords internal
 bivariate_ggplot_call <- function(x_class = c("NULL", "numeric", "integer", "factor", "character", "logical"),
                                   y_class = c("NULL", "numeric", "integer", "factor", "character", "logical"),
                                   freq = TRUE,
@@ -963,9 +957,7 @@ bivariate_ggplot_call <- function(x_class = c("NULL", "numeric", "integer", "fac
   plot_call
 }
 
-#' Create facet call
-#' @noRd
-#' @keywords internal
+# Create facet call
 facet_ggplot_call <- function(row_facet = character(0),
                               col_facet = character(0),
                               free_x_scales = FALSE,
@@ -996,8 +988,6 @@ facet_ggplot_call <- function(row_facet = character(0),
   }
 }
 
-#' @noRd
-#' @keywords internal
 coloring_ggplot_call <- function(colour,
                                  fill,
                                  size,

R/tm_g_distribution.R

@@ -1,4 +1,4 @@
-#' Distribution analysis module
+#' `teal` module: Distribution analysis
 #'
 #' Module is designed to explore the distribution of a single variable within a given dataset.
 #' It offers several tools, such as histograms, Q-Q plots, and various statistical tests to
@@ -25,6 +25,8 @@
 #' @templateVar ggnames "Histogram", "QQplot"
 #' @template ggplot2_args_multi
 #'
+#' @inherit shared_params return
+#'
 #' @examples
 #' library(teal.widgets)
 #'

R/tm_g_response.R

@@ -1,4 +1,4 @@
-#' Response plot module
+#' `teal` module: Response plot
 #'
 #' Generates a response plot for a given `response` and `x` variables.
 #' This module allows users customize and add annotations to the plot depending
@@ -422,7 +422,6 @@ srv_g_response <- function(id,
           env = list(resp_var = resp_var)
         )
       ) %>%
-        # nolint start
         # rowf and colf will be a NULL if not set by a user
         teal.code::eval_code(
           substitute(
@@ -442,7 +441,6 @@ srv_g_response <- function(id,
             env = list(x_cl = x_cl, rowf = rowf, colf = colf)
           )
         )
-      # nolint end
 
       plot_call <- substitute(
         expr = ggplot(ANL2, aes(x = x_cl, y = ns)) +

R/tm_g_scatterplot.R

@@ -1,4 +1,4 @@
-#' Scatterplot module
+#' `teal` module: Scatterplot
 #'
 #' Generates a customizable scatterplot using `ggplot2`.
 #' This module allows users to select variables for the x and y axes,
@@ -22,18 +22,14 @@
 #' Specifies the variable(s) for faceting rows.
 #' @param col_facet (`data_extract_spec` or `list` of multiple `data_extract_spec`, optional)
 #' Specifies the variable(s) for faceting columns.
-#' @param alpha (`numeric`, optional) Specifies point opacity.
-#' - If vector of `length == 1` then the plot points will have a fixed opacity.
-#' - while vector of `value`, `min`, and `max` allows dynamic adjustment.
-#' @param size (`numeric`, optional) Specifies point size.
-#' - If vector of `length == 1` then the plot point sizes will have a fixed size
-#' - while vector of `value`, `min`, and `max` allows dynamic adjustment.
 #' @param shape (`character`, optional) A character vector with the names of the
 #' shape, e.g. `c("triangle", "square", "circle")`. It defaults to `shape_names`. This is a complete list from
 #' `vignette("ggplot2-specs", package="ggplot2")`.
 #' @param max_deg (`integer`, optional) The maximum degree for the polynomial trend line. Must not be less than 1.
 #' @param table_dec (`integer`, optional) Number of decimal places used to round numeric values in the table.
 #'
+#' @inherit shared_params return
+#'
 #' @examples
 #' library(teal.widgets)
 #'

R/tm_g_scatterplotmatrix.R

@@ -1,4 +1,4 @@
-#' Scatterplot matrix module
+#' `teal` module: Scatterplot matrix
 #'
 #' Generates a scatterplot matrix from selected `variables` from datasets.
 #' Each plot within the matrix represents the relationship between two variables,
@@ -16,6 +16,8 @@
 #' `data_extract_spec` use `select_spec(..., ordered = TRUE)` if plot elements should be
 #' rendered according to selection order.
 #'
+#' @inherit shared_params return
+#'
 #' @examples
 #' # general data example
 #' data <- teal_data()
@@ -489,6 +491,7 @@ srv_g_scatterplotmatrix <- function(id, data, reporter, filter_panel_api, variab
 #' stats::cor.test(x, y, na.action = "na.fail")
 #' stats::cor.test(~ x + y,  na.action = "na.fail")
 #' ```
+#'
 #' @param x,y (`numeric`) vectors of data values. `x` and `y` must have the same length.
 #' @param .f (`function`) function that accepts x and y as formula input `~ x + y`.
 #' Default `stats::cor.test`.
@@ -497,6 +500,7 @@ srv_g_scatterplotmatrix <- function(id, data, reporter, filter_panel_api, variab
 #' @param round_pval (`integer(1)`) optional. Number of decimal places to use when rounding the p-value.
 #'
 #' @return Character with stats. For [stats::cor.test()] correlation coefficient and p-value.
+#'
 #' @examples
 #' set.seed(1)
 #' x <- runif(25, 0, 1)