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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
)

Arguments

label

menu item label of the module in the teal app.

dataname

analysis data passed to the data argument of teal init. E.g. ADaM structured laboratory data frame ADLB.

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.

Details

None

Author

Nick Paszty (npaszty) paszty.nicholas@gene.com

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

Examples


# Example using ADaM structure analysis dataset.

library(dplyr)
library(scda)

# original ARM value = dose value
arm_mapping <- list(
  "A: Drug X" = "150mg QD",
  "B: Placebo" = "Placebo",
  "C: Combination" = "Combination"
)

ADSL <- synthetic_cdisc_data("latest")$adsl
ADLB <- synthetic_cdisc_data("latest")$adlb
var_labels <- lapply(ADLB, function(x) attributes(x)$label)
ADLB <- ADLB %>%
  dplyr::mutate(
    AVISITCD = dplyr::case_when(
      AVISIT == "SCREENING" ~ "SCR",
      AVISIT == "BASELINE" ~ "BL",
      grepl("WEEK", AVISIT) ~ paste("W", stringr::str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
      TRUE ~ as.character(NA)
    ),
    AVISITCDN = dplyr::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 = dplyr::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"]]

app <- teal::init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"),
    cdisc_dataset(
      "ADLB",
      ADLB,
      code = [1416 chars quoted with '"'],
      vars = list(arm_mapping = arm_mapping)
    ),
    check = TRUE
  ),
  modules = modules(
    tm_g_gh_density_distribution_plot(
      label = "Density Distribution Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      xaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      color_manual = c(
        "150mg QD" = "#000000",
        "Placebo" = "#3498DB",
        "Combination" = "#E74C3C"
      ),
      color_comb = "#39ff14",
      comb_line = TRUE,
      plot_height = c(500, 200, 2000),
      font_size = c(12, 8, 20),
      line_size = c(1, .25, 3),
      hline_arb = c(.02, .05),
      hline_arb_color = c("red", "black"),
      hline_arb_label = c("Horizontal Line A", "Horizontal Line B")
    )
  )
)
#> [INFO] 2022-06-14 17:42:43.0414 pid:1172 token:[] teal.goshawk Initializing tm_g_gh_density_distribution_plot
if (FALSE) {
shinyApp(app$ui, app$server)
}