update goshawk v0.1.17 changes (#277)

part of : insightsengineering/goshawk#243

Exposed the `dot_size` argument in  `th_lineplot `and `th_spaghettiplot`

DESCRIPTION

@@ -29,7 +29,7 @@ URL: https://insightsengineering.github.io/teal.goshawk/,
     https://github.com/insightsengineering/teal.goshawk/
 BugReports: https://github.com/insightsengineering/teal.goshawk/issues
 Depends:
-    goshawk (>= 0.1.15.9007),
+    goshawk (>= 0.1.17),
     R (>= 3.6),
     shiny (>= 1.6.0),
     teal (>= 0.14.0.9027),

R/tm_g_gh_lineplot.R

@@ -41,6 +41,7 @@
 #' @param count_threshold minimum count of observations (as listed in the output table) to plot
 #' nodes on the graph
 #' @param table_font_size controls the font size of values in the table
+#' @param dot_size plot dot size.
 #' @param plot_relative_height_value numeric value between 500 and 5000 for controlling the starting value
 #' of the relative plot height slider
 #' @author Wenyi Liu (luiw2) wenyi.liu@roche.com
@@ -155,13 +156,26 @@ tm_g_gh_lineplot <- function(label,
                              post_output = NULL,
                              count_threshold = 0,
                              table_font_size = c(12, 4, 20),
+                             dot_size = c(2, 1, 12),
                              plot_relative_height_value = 1000) {
   message("Initializing tm_g_gh_lineplot")
+  # Validate string inputs
+  checkmate::assert_string(label)
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(param_var)
+  checkmate::assert_string(param_var_label)
+  checkmate::assert_string(stat)
+
+  # Validate choices_selected class inputs
   checkmate::assert_class(param, "choices_selected")
   checkmate::assert_class(xaxis_var, "choices_selected")
   checkmate::assert_class(yaxis_var, "choices_selected")
   checkmate::assert_class(trt_group, "choices_selected")
+
+  # Validate flag inputs
   checkmate::assert_flag(rotate_xlab)
+
+  # Validate numeric vector inputs
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
   checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
   checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
@@ -170,16 +184,23 @@ tm_g_gh_lineplot <- function(label,
     lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
   )
   checkmate::assert_numeric(table_font_size, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
+  checkmate::assert_numeric(dot_size, len = 3)
   checkmate::assert_numeric(
     table_font_size[1],
     lower = table_font_size[2], upper = table_font_size[3],
     null.ok = TRUE, .var.name = "table_font_size"
   )
-
   checkmate::assert_number(plot_relative_height_value, lower = 500, upper = 5000)
-
   checkmate::assert_number(count_threshold)
+
+  # Validate color manual if provided
+  checkmate::assert_character(color_manual, null.ok = TRUE)
+  checkmate::assert_character(hline_arb_color)
+  checkmate::assert_character(hline_arb_label)
+
+  # Validate line arguments
   validate_line_arb_arg(hline_arb, hline_arb_color, hline_arb_label)
+
   args <- as.list(environment())
 
   module(
@@ -284,6 +305,12 @@ ui_lineplot <- function(id, ...) {
               "Font Size",
               a$plot_font_size,
               ticks = FALSE
+            ),
+            teal.widgets::optionalSliderInputValMinMax(
+              ns("dot_size"),
+              "Dot Size",
+              a$dot_size,
+              ticks = FALSE
             )
           ),
           teal.widgets::panel_item(
@@ -647,6 +674,7 @@ srv_lineplot <- function(id,
       # nolint start
       ylim <- yrange_slider$state()$value
       plot_font_size <- input$plot_font_size
+      dot_size <- input$dot_size
       dodge <- input$dodge
       rotate_xlab <- input$rotate_xlab
       count_threshold <- `if`(is.na(as.numeric(input$count_threshold)), 0, as.numeric(input$count_threshold))
@@ -730,6 +758,7 @@ srv_lineplot <- function(id,
             rotate_xlab = .(rotate_xlab),
             plot_height = .(relative_height), # in g_lineplot this is relative height of plot to table
             plot_font_size = .(plot_font_size),
+            dot_size = .(dot_size),
             dodge = .(dodge),
             count_threshold = .(count_threshold),
             table_font_size = .(table_font_size),

R/tm_g_gh_spaghettiplot.R

@@ -35,6 +35,7 @@
 #' @param plot_height controls plot height.
 #' @param plot_width optional, controls plot width.
 #' @param font_size control font size for title, `x-axis`, `y-axis` and legend font.
+#' @param dot_size plot dot size.
 #' @param group_stats control group mean or median overlay.
 #' @param hline_arb numeric vector of at most 2 values identifying intercepts for arbitrary horizontal lines.
 #' @param hline_arb_color a character vector of at most length of \code{hline_arb}.
@@ -181,6 +182,7 @@ tm_g_gh_spaghettiplot <- function(label,
                                   plot_height = c(600, 200, 2000),
                                   plot_width = NULL,
                                   font_size = c(12, 8, 20),
+                                  dot_size = c(2, 1, 12),
                                   hline_arb = numeric(0),
                                   hline_arb_color = "red",
                                   hline_arb_label = "Horizontal line",
@@ -190,20 +192,49 @@ tm_g_gh_spaghettiplot <- function(label,
                                   pre_output = NULL,
                                   post_output = NULL) {
   message("Initializing tm_g_gh_spaghettiplot")
+
+  # Validate string inputs
+  checkmate::assert_string(label)
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(param_var)
+  checkmate::assert_string(param_var_label)
+  checkmate::assert_string(idvar)
+  checkmate::assert_string(group_stats)
+
+  # Validate choices_selected class inputs
   checkmate::assert_class(param, "choices_selected")
   checkmate::assert_class(xaxis_var, "choices_selected")
   checkmate::assert_class(yaxis_var, "choices_selected")
   checkmate::assert_class(trt_group, "choices_selected")
-  validate_line_arb_arg(hline_arb, hline_arb_color, hline_arb_label)
-  validate_line_vars_arg(hline_vars, hline_vars_colors, hline_vars_labels)
+
+  # Validate flag inputs
+  checkmate::assert_flag(rotate_xlab)
+  checkmate::assert_flag(free_x)
+
+  # Validate numeric vector inputs
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
   checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
   checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
-  checkmate::assert_numeric(plot_width[1],
-    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE,
-    .var.name = "plot_width"
+  checkmate::assert_numeric(
+    plot_width[1],
+    lower = plot_width[2], upper = plot_width[3],
+    null.ok = TRUE, .var.name = "plot_width"
   )
-  checkmate::assert_flag(free_x)
+  checkmate::assert_numeric(font_size, len = 3, any.missing = FALSE, finite = TRUE)
+  checkmate::assert_numeric(dot_size, len = 3, any.missing = FALSE, finite = TRUE)
+
+  # Validate color manual if provided
+  checkmate::assert_character(man_color, null.ok = TRUE)
+  checkmate::assert_character(color_comb, null.ok = TRUE)
+  checkmate::assert_character(hline_arb_color)
+  checkmate::assert_character(hline_arb_label)
+
+  # Validate facet columns
+  checkmate::assert_int(facet_ncol, lower = 1)
+
+  # Validate line arguments
+  validate_line_arb_arg(hline_arb, hline_arb_color, hline_arb_label)
+  validate_line_vars_arg(hline_vars, hline_vars_colors, hline_vars_labels)
 
   args <- as.list(environment())
 
@@ -298,6 +329,7 @@ g_ui_spaghettiplot <- function(id, ...) {
             checkboxInput(ns("free_x"), "Free X-Axis Scales", a$free_x),
             checkboxInput(ns("rotate_xlab"), "Rotate X-Axis Label", a$rotate_xlab),
             teal.widgets::optionalSliderInputValMinMax(ns("font_size"), "Font Size", a$font_size, ticks = FALSE),
+            teal.widgets::optionalSliderInputValMinMax(ns("dot_size"), "Dot Size", a$dot_size, ticks = FALSE),
             teal.widgets::optionalSliderInputValMinMax(
               ns("alpha"),
               "Line Alpha",
@@ -408,6 +440,7 @@ srv_g_spaghettiplot <- function(id,
       hline_arb_color <- horizontal_line()$line_arb_color
       group_stats <- input$group_stats
       font_size <- input$font_size
+      dot_size <- input$dot_size
       alpha <- input$alpha
       validate(need(input$trt_group, "Please select a treatment variable"))
       trt_group <- input$trt_group
@@ -473,6 +506,7 @@ srv_g_spaghettiplot <- function(id,
             xlabel = xlabel,
             rotate_xlab = .(rotate_xlab),
             font_size = .(font_size),
+            dot_size = .(dot_size),
             alpha = .(alpha),
             group_stats = .(group_stats),
             hline_vars = .(hline_vars),

README.md

@@ -1,7 +1,6 @@
 # teal.goshawk
 
 <!-- start badges -->
-[![Check 🛠](https://github.com/insightsengineering/teal.goshawk/actions/workflows/check.yaml/badge.svg)](https://insightsengineering.github.io/teal.goshawk/main/unit-test-report/)
 [![Docs 📚](https://github.com/insightsengineering/teal.goshawk/actions/workflows/docs.yaml/badge.svg)](https://insightsengineering.github.io/teal.goshawk/)
 [![Code Coverage 📔](https://raw.githubusercontent.com/insightsengineering/teal.goshawk/_xml_coverage_reports/data/main/badge.svg)](https://insightsengineering.github.io/teal.goshawk/main/coverage-report/)
 

vignettes/teal-goshawk.Rmd

@@ -22,7 +22,7 @@ standards. `teal.goshawk` modules can be used with data other than `ADaM` standa
 features of the package will likely not be applicable.
 
 The concepts presented here require knowledge about the core features of `teal`, specifically on how to launch a `teal`
-application and how to pass data into it. Therefore, it is highly recommended to refer to the [`README`](https://insightsengineering.github.io/teal/) file and the introductory [`vignette`](https://insightsengineering.github.io/teal/latest-tag/articles/teal.html) of the `teal` package.
+application and how to pass data into it. Therefore, it is highly recommended to refer to the [`README`](https://insightsengineering.github.io/teal/latest-tag/) file and the introductory [`vignette`](https://insightsengineering.github.io/teal/latest-tag/articles/index.html) of the `teal` package.
 
 ### Main features
 
@@ -108,4 +108,4 @@ Refer to the [Get Started](https://insightsengineering.github.io/teal.modules.cl
 section of the teal.modules.clinical package that provides additional detail on `teal` concepts as applied in another simple app
 example.
 
-Please see additional information under [Articles](https://insightsengineering.github.io/teal.goshawk/latest-tag/articles) for data expectations, requirements and pre/post-processing rationale
+Please see additional information under [Articles](https://insightsengineering.github.io/teal.goshawk/latest-tag/articles/index.html) for data expectations, requirements and pre/post-processing rationale