Spaghetti Plot — tm_g_gh_spaghettiplot • teal.goshawk

This teal module renders the UI and calls the function that creates a spaghetti plot.

Usage

tm_g_gh_spaghettiplot(
  label,
  dataname,
  param_var,
  param,
  param_var_label = "PARAM",
  idvar,
  xaxis_var,
  yaxis_var,
  xaxis_var_level = NULL,
  filter_var = yaxis_var,
  trt_group,
  trt_group_level = NULL,
  group_stats = "NONE",
  man_color = NULL,
  color_comb = NULL,
  xtick = ggplot2::waiver(),
  xlabel = xtick,
  rotate_xlab = FALSE,
  facet_ncol = 2,
  free_x = FALSE,
  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",
  hline_vars = character(0),
  hline_vars_colors = "green",
  hline_vars_labels = hline_vars,
  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 laboratory data frame ADLB.
param_var: name of variable containing biomarker codes e.g. PARAMCD.
param: biomarker selected.
param_var_label: single name of variable in analysis data that includes parameter labels.
idvar: name of unique subject id variable.
xaxis_var: single name of variable in analysis data that is used as x-axis in the plot for the respective goshawk function.
yaxis_var: single name of variable in analysis data that is used as summary variable in the respective goshawk function.
xaxis_var_level: vector that can be used to define the factor level of xaxis_var. Only use it when xaxis_var is character or factor.
filter_var: data constraint variable.
trt_group: choices_selected object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.
trt_group_level: vector that can be used to define factor level of trt_group.
group_stats: control group mean or median overlay.
man_color: string vector representing customized colors
color_comb: name or hex value for combined treatment color.
xtick: numeric vector to define the tick values of x-axis when x variable is numeric. Default value is waive().
xlabel: vector with same length of xtick to define the label of x-axis tick values. Default value is waive().
rotate_xlab: logical(1) value indicating whether to rotate x-axis labels
facet_ncol: numeric value indicating number of facets per row.
free_x: logical(1) should scales be "fixed" (FALSE) of "free" (TRUE) for x-axis in facet_wrap scales parameter.
plot_height: controls plot height.
plot_width: optional, controls plot width.
font_size: control font size for title, x-axis, y-axis and legend font.
dot_size: plot dot size.
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.
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").

Value

shiny object

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

Wenyi Liu (luiw2) wenyi.liu@roche.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)

  # use non-exported function from goshawk
  .h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")

  # 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),
      ANRLO = 30,
      ANRHI = 75
    ) %>%
    rowwise() %>%
    group_by(PARAMCD) %>%
    mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE),
      paste("<", round(runif(1, min = 25, max = 30))), LBSTRESC
    )) %>%
    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 <- .h_identify_loq_values(ADLB, "LOQFL")
  ADLB <- left_join(ADLB, ALB_LOQS, by = "PARAM")
})

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

app <- init(
  data = data,
  modules = modules(
    tm_g_gh_spaghettiplot(
      label = "Spaghetti Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      idvar = "USUBJID",
      xaxis_var = choices_selected(c("Analysis Visit Code" = "AVISITCD"), "AVISITCD"),
      yaxis_var = choices_selected(c("AVAL", "CHG", "PCHG"), "AVAL"),
      filter_var = choices_selected(
        c("None" = "NONE", "Screening" = "BASE2", "Baseline" = "BASE"),
        "NONE"
      ),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      color_comb = "#39ff14",
      man_color = c(
        "Combination" = "#000000",
        "Placebo" = "#fce300",
        "150mg QD" = "#5a2f5f"
      ),
      hline_arb = c(60, 50),
      hline_arb_color = c("grey", "red"),
      hline_arb_label = c("default A", "default B"),
      hline_vars = c("ANRHI", "ANRLO", "ULOQN", "LLOQN"),
      hline_vars_colors = c("pink", "brown", "purple", "black"),
    )
  )
)
#> Initializing tm_g_gh_spaghettiplot
if (interactive()) {
  shinyApp(app$ui, app$server)
}