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 = "ADLB",
  param_var = lifecycle::deprecated(),
  param = teal.picks::picks(teal.picks::variables("PARAMCD", "PARAMCD"),
    teal.picks::values(selected = "ALT", multiple = FALSE), check_dataset = FALSE),
  param_var_label = "PARAM",
  idvar = "USUBJID",
  xaxis_var = teal.picks::variables(c("AVISITCD", "AVISIT"), "AVISITCD"),
  yaxis_var = teal.picks::variables(c("AVAL", "CHG", "PCHG"), "AVAL"),
  xaxis_var_level = NULL,
  filter_var = lifecycle::deprecated(),
  trt_group = teal.picks::variables(dplyr::starts_with("ARM"), selected = "ARM"),
  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,
  alpha = c(0.8, 0, 1),
  pre_output = NULL,
  post_output = NULL,
  transformators = list(),
  decorators = 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

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

param

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

param_var_label

(character(1)) single name of variable in analysis data that includes parameter labels.

idvar

name of unique subject id variable.

xaxis_var

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

yaxis_var

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

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

(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.

trt_group_level

(named character()) 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()) numeric vector to define the tick values of x-axis when x variable is numeric. Default value is waive().

xlabel

(character()) vector with same length of xtick to define the label of x-axis tick values. Default value is waive().

rotate_xlab

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

facet_ncol

(integer(1)) 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

(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.

dot_size

(numeric(3)) plot dot size.

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.

hline_vars

(character) a character vector to name the columns that will define additional horizontal lines.

hline_vars_colors

(character) a character vector naming the colors for the additional horizontal lines.

hline_vars_labels

(character) a character vector naming the labels for the additional horizontal lines that will appear in the plot.

alpha

(numeric(3)) 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.

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_spaghettiplot(
   ..., # 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

Wenyi Liu

Balazs Toth

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"
  )
  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),
      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 = picks(
        variables("PARAMCD", "PARAMCD"),
        values(selected = "ALT", multiple = FALSE),
        check_dataset = FALSE
      ),
      idvar = "USUBJID",
      xaxis_var = variables(c("AVISITCD", "AVISIT"), "AVISITCD"),
      yaxis_var = variables(c("AVAL", "CHG", "PCHG"), "AVAL"),
      trt_group = variables(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
#> 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)
}