Merge branch 'main' into 712-tm_a_pca@main

insightsengineering · Apr 22, 2024 · aa9d18c · aa9d18c
2 parents 7099007 + 9e5c0aa
commit aa9d18c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: teal.modules.general
 Title: General Modules for 'teal' Applications
-Version: 0.3.0.9017
+Version: 0.3.0.9021
 Date: 2024-04-19
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# teal.modules.general 0.3.0.9017
+# teal.modules.general 0.3.0.9021
 
 # teal.modules.general 0.3.0
 

diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
@@ -56,52 +56,49 @@
 #'   CO2 <- data.frame(CO2)
 #' })
 #' datanames(data) <- c("CO2")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
 #'
 #' app <- init(
 #'   data = data,
-#'   modules = modules(
-#'     tm_g_bivariate(
-#'       x = data_extract_spec(
-#'         dataname = "CO2",
-#'         select = select_spec(
-#'           label = "Select variable:",
-#'           choices = variable_choices(data[["CO2"]]),
-#'           selected = "conc",
-#'           fixed = FALSE
-#'         )
-#'       ),
-#'       y = data_extract_spec(
-#'         dataname = "CO2",
-#'         select = select_spec(
-#'           label = "Select variable:",
-#'           choices = variable_choices(data[["CO2"]]),
-#'           selected = "uptake",
-#'           multiple = FALSE,
-#'           fixed = FALSE
-#'         )
-#'       ),
-#'       row_facet = data_extract_spec(
-#'         dataname = "CO2",
-#'         select = select_spec(
-#'           label = "Select variable:",
-#'           choices = variable_choices(data[["CO2"]]),
-#'           selected = "Type",
-#'           fixed = FALSE
-#'         )
-#'       ),
-#'       col_facet = data_extract_spec(
-#'         dataname = "CO2",
-#'         select = select_spec(
-#'           label = "Select variable:",
-#'           choices = variable_choices(data[["CO2"]]),
-#'           selected = "Treatment",
-#'           fixed = FALSE
-#'         )
-#'       ),
-#'       ggplot2_args = ggplot2_args(
-#'         labs = list(subtitle = "Plot generated by Bivariate Module")
+#'   modules = tm_g_bivariate(
+#'     x = data_extract_spec(
+#'       dataname = "CO2",
+#'       select = select_spec(
+#'         label = "Select variable:",
+#'         choices = variable_choices(data[["CO2"]]),
+#'         selected = "conc",
+#'         fixed = FALSE
+#'       )
+#'     ),
+#'     y = data_extract_spec(
+#'       dataname = "CO2",
+#'       select = select_spec(
+#'         label = "Select variable:",
+#'         choices = variable_choices(data[["CO2"]]),
+#'         selected = "uptake",
+#'         multiple = FALSE,
+#'         fixed = FALSE
+#'       )
+#'     ),
+#'     row_facet = data_extract_spec(
+#'       dataname = "CO2",
+#'       select = select_spec(
+#'         label = "Select variable:",
+#'         choices = variable_choices(data[["CO2"]]),
+#'         selected = "Type",
+#'         fixed = FALSE
+#'       )
+#'     ),
+#'     col_facet = data_extract_spec(
+#'       dataname = "CO2",
+#'       select = select_spec(
+#'         label = "Select variable:",
+#'         choices = variable_choices(data[["CO2"]]),
+#'         selected = "Treatment",
+#'         fixed = FALSE
 #'       )
+#'     ),
+#'     ggplot2_args = ggplot2_args(
+#'       labs = list(subtitle = "Plot generated by Bivariate Module")
 #'     )
 #'   )
 #' )
@@ -121,48 +118,46 @@
 #'
 #' app <- init(
 #'   data = data,
-#'   modules = modules(
-#'     tm_g_bivariate(
-#'       x = data_extract_spec(
-#'         dataname = "ADSL",
-#'         select = select_spec(
-#'           label = "Select variable:",
-#'           choices = variable_choices(data[["ADSL"]]),
-#'           selected = "AGE",
-#'           fixed = FALSE
-#'         )
-#'       ),
-#'       y = data_extract_spec(
-#'         dataname = "ADSL",
-#'         select = select_spec(
-#'           label = "Select variable:",
-#'           choices = variable_choices(data[["ADSL"]]),
-#'           selected = "SEX",
-#'           multiple = FALSE,
-#'           fixed = FALSE
-#'         )
-#'       ),
-#'       row_facet = data_extract_spec(
-#'         dataname = "ADSL",
-#'         select = select_spec(
-#'           label = "Select variable:",
-#'           choices = variable_choices(data[["ADSL"]]),
-#'           selected = "ARM",
-#'           fixed = FALSE
-#'         )
-#'       ),
-#'       col_facet = data_extract_spec(
-#'         dataname = "ADSL",
-#'         select = select_spec(
-#'           label = "Select variable:",
-#'           choices = variable_choices(data[["ADSL"]]),
-#'           selected = "COUNTRY",
-#'           fixed = FALSE
-#'         )
-#'       ),
-#'       ggplot2_args = ggplot2_args(
-#'         labs = list(subtitle = "Plot generated by Bivariate Module")
+#'   modules = tm_g_bivariate(
+#'     x = data_extract_spec(
+#'       dataname = "ADSL",
+#'       select = select_spec(
+#'         label = "Select variable:",
+#'         choices = variable_choices(data[["ADSL"]]),
+#'         selected = "AGE",
+#'         fixed = FALSE
 #'       )
+#'     ),
+#'     y = data_extract_spec(
+#'       dataname = "ADSL",
+#'       select = select_spec(
+#'         label = "Select variable:",
+#'         choices = variable_choices(data[["ADSL"]]),
+#'         selected = "SEX",
+#'         multiple = FALSE,
+#'         fixed = FALSE
+#'       )
+#'     ),
+#'     row_facet = data_extract_spec(
+#'       dataname = "ADSL",
+#'       select = select_spec(
+#'         label = "Select variable:",
+#'         choices = variable_choices(data[["ADSL"]]),
+#'         selected = "ARM",
+#'         fixed = FALSE
+#'       )
+#'     ),
+#'     col_facet = data_extract_spec(
+#'       dataname = "ADSL",
+#'       select = select_spec(
+#'         label = "Select variable:",
+#'         choices = variable_choices(data[["ADSL"]]),
+#'         selected = "COUNTRY",
+#'         fixed = FALSE
+#'       )
+#'     ),
+#'     ggplot2_args = ggplot2_args(
+#'       labs = list(subtitle = "Plot generated by Bivariate Module")
 #'     )
 #'   )
 #' )
@@ -666,7 +661,12 @@ srv_g_bivariate <- function(id,
           expr = {
             # Add facetting labels
             # optional: grid.newpage() # nolint: commented_code.
-            p <- add_facet_labels(p, xfacet_label = nulled_col_facet_name, yfacet_label = nulled_row_facet_name)
+            # Prefixed with teal.modules.general as its usage will appear in "Show R code"
+            p <- teal.modules.general::add_facet_labels(
+              p,
+              xfacet_label = nulled_col_facet_name,
+              yfacet_label = nulled_row_facet_name
+            )
             grid::grid.newpage()
             grid::grid.draw(p)
           },

diff --git a/R/tm_missing_data.R b/R/tm_missing_data.R
@@ -730,7 +730,11 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
               values = c("grey90", c(getOption("ggplot2.discrete.colour")[2], "#ff2951ff")[1]),
               labels = c("Present", "Missing")
             ) +
-            scale_y_continuous(labels = scales::percent_format(), breaks = seq(0, 1, by = 0.1), expand = c(0, 0)) +
+            scale_y_continuous(
+              labels = scales::percent_format(),
+              breaks = seq(0, 1, by = 0.1),
+              expand = c(0, 0)
+            ) +
             geom_text(
               aes(label = ifelse(isna == TRUE, sprintf("%d [%.02f%%]", n, n_pct), ""), y = 1),
               hjust = 1,
@@ -803,7 +807,11 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
                 fill = ~isna
               ) +
               geom_bar(alpha = 1, stat = "identity", position = "fill") +
-              scale_y_continuous(labels = scales::percent_format(), breaks = seq(0, 1, by = 0.1), expand = c(0, 0)) +
+              scale_y_continuous(
+                labels = scales::percent_format(),
+                breaks = seq(0, 1, by = 0.1),
+                expand = c(0, 0)
+              ) +
               scale_fill_manual(
                 name = "",
                 values = c("grey90", c(getOption("ggplot2.discrete.colour")[2], "#ff2951ff")[1]),
@@ -972,7 +980,11 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
               dplyr::distinct() %>%
               ggplot(aes(x = id, y = n)) +
               geom_bar(stat = "identity", fill = c(getOption("ggplot2.discrete.colour")[2], "#ff2951ff")[1]) +
-              geom_text(aes(label = n), position = position_dodge(width = 0.9), vjust = -0.25) +
+              geom_text(
+                aes(label = n),
+                position = position_dodge(width = 0.9),
+                vjust = -0.25
+              ) +
               ylim(c(0, max(data_combination_plot_cutoff$n) * 1.5)) +
               labs1 +
               ggthemes1 +