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,
  param_var,
  param,
  xaxis_var,
  trt_group,
  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()
)

Arguments

label: menu item label of the module in the teal app.
dataname: analysis data passed to the data argument of init. E.g. ADaM structured
param_var: name of variable containing biomarker codes e.g. PARAMCD.
param: biomarker selected.
xaxis_var: name of variable containing biomarker results displayed on x-axis e.g. BASE.
trt_group: choices_selected object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.
color_manual: vector of colors applied to treatment values.
color_comb: name or hex value for combined treatment color.
plot_height: controls plot height.
plot_width: optional, controls plot width.
font_size: 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: a character vector of at most length of hline_arb. naming the color for the arbitrary horizontal lines.
hline_arb_label: a character vector of at most length of hline_arb. naming the label for the arbitrary horizontal lines.
facet_ncol: numeric value indicating number of facets per row.
comb_line: display combined treatment line toggle.
rotate_xlab: 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").

Details

None

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 (npaszty) paszty.nicholas@gene.com

Balazs Toth (tothb2) toth.balazs@gene.com

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"
  )
  set.seed(1) # @linksto ADSL ADLB
  ADSL <- rADSL
  ADLB <- 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_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      xaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = choices_selected(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
if (interactive()) {
  shinyApp(app$ui, app$server)
}