Box Plot — tm_g_gh_boxplot • teal.goshawk

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

Usage

tm_g_gh_boxplot(
  label,
  dataname,
  param_var,
  param,
  yaxis_var = teal.transform::choices_selected(c("AVAL", "CHG"), "AVAL"),
  xaxis_var = teal.transform::choices_selected("AVISITCD", "AVISITCD"),
  facet_var = teal.transform::choices_selected(c("ARM", "ACTARM"), "ARM"),
  trt_group,
  color_manual = NULL,
  shape_manual = NULL,
  facet_ncol = NULL,
  loq_legend = TRUE,
  rotate_xlab = FALSE,
  hline_arb = numeric(0),
  hline_arb_color = "red",
  hline_arb_label = "Horizontal line",
  hline_vars = character(0),
  hline_vars_colors = "green",
  hline_vars_labels = hline_vars,
  plot_height = c(600, 200, 2000),
  plot_width = NULL,
  font_size = c(12, 8, 20),
  dot_size = c(2, 1, 12),
  alpha = c(0.8, 0, 1),
  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 ALB.
param_var: name of variable containing biomarker codes e.g. PARAMCD.
param: list of biomarkers of interest.
yaxis_var: name of variable containing biomarker results displayed on y-axis e.g. AVAL. When not provided, it defaults to choices_selected(c("AVAL", "CHG"), "AVAL").
xaxis_var: variable to categorize the x-axis. When not provided, it defaults to choices_selected("AVISITCD", "AVISITCD").
facet_var: variable to facet the plots by. When not provided, it defaults to choices_selected(c("ARM", "ACTARM"), "ARM").
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.
shape_manual: vector of symbols applied to LOQ values.
facet_ncol: numeric value indicating number of facets per row.
loq_legend: loq legend toggle.
rotate_xlab: 45 degree rotation of x-axis values.
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.
hline_vars: a character vector to name the columns that will define additional horizontal lines.
hline_vars_colors: a character vector naming the colors for the additional horizontal lines.
hline_vars_labels: a character vector naming the labels for the additional horizontal lines that will appear in the legend.
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.
dot_size: plot dot size.
alpha: numeric vector to define transparency of plotted points.
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.

Value

an module object

Author

Jeff Tomlinson (tomlinsj) jeffrey.tomlinson@roche.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"
)

set.seed(1)
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),
    ANRLO = 50,
    ANRHI = 75
  ) %>%
  dplyr::rowwise() %>%
  dplyr::group_by(PARAMCD) %>%
  dplyr::mutate(LBSTRESC = ifelse(
    USUBJID %in% sample(USUBJID, 1, replace = TRUE),
    paste("<", round(runif(1, min = 25, max = 30))), LBSTRESC
  )) %>%
  dplyr::mutate(LBSTRESC = ifelse(
    USUBJID %in% sample(USUBJID, 1, replace = TRUE),
    paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC
  )) %>%
  ungroup()

attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"

# add LLOQ and ULOQ variables
ALB_LOQS <- goshawk:::h_identify_loq_values(ADLB)
ADLB <- left_join(ADLB, ALB_LOQS, by = "PARAM")

app <- teal::init(
  data = cdisc_data(
    adsl <- cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"),
    cdisc_dataset(
      "ADLB",
      ADLB,
      code = [2091 chars quoted with '"'],
      vars = list(ADSL = adsl, arm_mapping = arm_mapping)
    ),
    check = TRUE
  ),
  modules = modules(
    tm_g_gh_boxplot(
      label = "Box Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      yaxis_var = choices_selected(c("AVAL", "BASE", "CHG"), "AVAL"),
      xaxis_var = choices_selected(c("ACTARM", "ARM", "AVISITCD", "STUDYID"), "ARM"),
      facet_var = choices_selected(c("ACTARM", "ARM", "AVISITCD", "SEX"), "AVISITCD"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      loq_legend = TRUE,
      rotate_xlab = FALSE,
      hline_arb = c(60, 55),
      hline_arb_color = c("grey", "red"),
      hline_arb_label = c("default_hori_A", "default_hori_B"),
      hline_vars = c("ANRHI", "ANRLO", "ULOQN", "LLOQN"),
      hline_vars_colors = c("pink", "brown", "purple", "black"),
    )
  )
)
#> [INFO] 2022-06-14 17:42:29.9968 pid:1172 token:[] teal.goshawk Initializing tm_g_gh_boxplot
if (FALSE) {
shinyApp(app$ui, app$server)
}