Density Distribution Plot — tm_g_gh_density_distribution

This teal module renders the UI and calls the functions that create a density distribution plot and an accompanying summary table.

Usage

tm_g_gh_density_distribution_plot(
  label,
  dataname = "ADLB",
  param_var = lifecycle::deprecated(),
  param = teal.picks::picks(teal.picks::variables("PARAMCD", "PARAMCD"),
    teal.picks::values(selected = "ALT", multiple = FALSE), check_dataset = FALSE),
  xaxis_var = teal.picks::variables(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
  trt_group = teal.picks::variables(dplyr::starts_with("ARM"), selected = "ARM"),
  color_manual = NULL,
  color_comb = NULL,
  plot_height = c(500, 200, 2000),
  plot_width = NULL,
  font_size = c(12, 8, 20),
  line_size = c(1, 0.25, 3),
  hline_arb = numeric(0),
  hline_arb_color = "red",
  hline_arb_label = "Horizontal line",
  facet_ncol = 2L,
  comb_line = TRUE,
  rotate_xlab = FALSE,
  pre_output = NULL,
  post_output = NULL,
  transformators = list(),
  decorators = list()
)

Arguments

label

(character(1)) menu item label of the module in the teal app.

dataname

(character(1)) analysis data passed to the data argument of teal::init(). E.g. ADaM structured laboratory data frame ADLB.

param_var

(character(1)) name of variable containing biomarker codes e.g. PARAMCD.

param

(teal.picks::picks() or teal.transform::choices_selected()) biomarker selected.

xaxis_var

(teal.picks::variables() or legacy teal.transform::choices_selected()) name of variable containing biomarker results displayed on x-axis e.g. BASE.

trt_group

(teal.picks::variables() or legacy teal.transform::choices_selected()) object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.

color_manual

(named character, optional) vector of colors applied to treatment values.

color_comb

name or hex value for combined treatment color.

plot_height

(numeric(3)) controls plot height.

plot_width

(numeric(3), optional) controls plot width.

font_size

(numeric(3)) font size control for title, x-axis label, y-axis label and legend.

line_size

plot line thickness.

hline_arb

(numeric) vector of at most 2 values identifying intercepts for arbitrary horizontal lines.

hline_arb_color

(character) a character vector of at most length of hline_arb. naming the color for the arbitrary horizontal lines.

hline_arb_label

(character) a character vector of at most length of hline_arb. naming the label for the arbitrary horizontal lines.

facet_ncol

(integer(1)) numeric value indicating number of facets per row.

comb_line

display combined treatment line toggle.

rotate_xlab

(logical(1)) 45 degree rotation of x-axis values.

pre_output

(shiny.tag) optional,
with text placed before the output to put the output into context. For example a title.

post_output

(shiny.tag) optional, with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

transformators

(list of teal_transform_module) that will be applied to transform module's data input. To learn more check vignette("transform-input-data", package = "teal").

decorators

(named list of lists of teal_transform_module) optional, decorator for tables or plots included in the module output reported. The decorators are applied to the respective output objects.

See section "Decorating Module" below for more details.

Value

A teal::module() object that can be used in a teal::init() call.

Decorating Module

This module generates the following objects, which can be modified in place using decorators:

plot (ggplot)

A Decorator is applied to the specific output using a named list of teal_transform_module objects. The name of this list corresponds to the name of the output to which the decorator is applied. See code snippet below:

tm_g_gh_density_distribution_plot(
   ..., # arguments for module
   decorators = list(
     plot = teal_transform_module(...) # applied only to `plot` output
   )
)

For additional details and examples of decorators, refer to the vignette vignette("decorate-module-output", package = "teal.goshawk").

To learn more please refer to the vignette vignette("transform-module-output", package = "teal") or the teal::teal_transform_module() documentation.

Reporting

This module returns an object of class teal_module, that contains a server function. Since the server function returns a teal_report object, this makes this module reportable, which means that the reporting functionality will be turned on automatically by the teal framework.

For more information on reporting in teal, see the vignettes:

vignette("reportable-shiny-application", package = "teal.reporter")
vignette("adding-support-for-reporting-to-custom-modules", package = "teal")

Author

Nick Paszty

Balazs Toth

Examples

# Example using ADaM structure analysis dataset.
data <- teal_data()
data <- within(data, {
  library(dplyr)
  library(stringr)

  # original ARM value = dose value
  .arm_mapping <- list(
    "A: Drug X" = "150mg QD",
    "B: Placebo" = "Placebo",
    "C: Combination" = "Combination"
  )
  ADSL <- teal.data::rADSL
  ADLB <- teal.data::rADLB
  .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
  ADLB <- ADLB %>%
    mutate(
      AVISITCD = case_when(
        AVISIT == "SCREENING" ~ "SCR",
        AVISIT == "BASELINE" ~ "BL",
        grepl("WEEK", AVISIT) ~ paste("W", str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
        TRUE ~ as.character(NA)
      ),
      AVISITCDN = case_when(
        AVISITCD == "SCR" ~ -2,
        AVISITCD == "BL" ~ 0,
        grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
        TRUE ~ as.numeric(NA)
      ),
      AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
      TRTORD = case_when(
        ARMCD == "ARM C" ~ 1,
        ARMCD == "ARM B" ~ 2,
        ARMCD == "ARM A" ~ 3
      ),
      ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]),
      ARM = factor(ARM) %>% reorder(TRTORD),
      ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]),
      ACTARM = factor(ACTARM) %>% reorder(TRTORD)
    )

  attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
  attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]]
})

join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_g_gh_density_distribution_plot(
      label = "Density Distribution Plot",
      dataname = "ADLB",
      param = picks(
        variables("PARAMCD", "PARAMCD"),
        values(selected = "ALT", multiple = FALSE),
        check_dataset = FALSE
      ),
      xaxis_var = variables(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = variables(c("ARM", "ACTARM"), "ARM"),
      color_manual = c(
        "150mg QD" = "#000000",
        "Placebo" = "#3498DB",
        "Combination" = "#E74C3C"
      ),
      color_comb = "#39ff14",
      comb_line = TRUE,
      plot_height = c(500, 200, 2000),
      font_size = c(12, 8, 20),
      line_size = c(1, .25, 3),
      hline_arb = c(.02, .05),
      hline_arb_color = c("red", "black"),
      hline_arb_label = c("Horizontal Line A", "Horizontal Line B")
    )
  )
)
#> Initializing tm_g_gh_density_distribution_plot
#> Warning: rlang::dots_list(..., .ignore_empty = "trailing")
#>  - Setting explicit `selected` while `choices` are delayed (set using `tidyselect`) doesn't guarantee that `selected` is a subset of `choices`.
if (interactive()) {
  shinyApp(app$ui, app$server)
}