Teal Module for Waterfall Plot — tm_g

This is teal module that generates a waterfall plot for ADaM data

Usage

tm_g_waterfall(
  label,
  dataname_tr = "ADTR",
  dataname_rs = "ADRS",
  bar_paramcd,
  bar_var,
  bar_color_var,
  bar_color_opt = NULL,
  sort_var,
  add_label_var_sl,
  add_label_paramcd_rs,
  anno_txt_var_sl,
  anno_txt_paramcd_rs,
  facet_var,
  ytick_at = 20,
  href_line = NULL,
  gap_point_val = NULL,
  show_value = TRUE,
  plot_height = c(1200L, 400L, 5000L),
  plot_width = NULL,
  pre_output = NULL,
  post_output = NULL
)

Arguments

label: (character(1))
menu item label of the module in the teal app.
dataname_tr: tumor burden analysis data used in teal module to plot as bar height, needs to be available in the list passed to the data argument of init
dataname_rs: response analysis data used in teal module to label response parameters, needs to be available in the list passed to the data argument of init
bar_paramcd: (choices_selected) parameter in tumor burden data that will be plotted as bar height
bar_var: (choices_selected) numeric variable from dataset to plot the bar height, e.g., PCHG
bar_color_var: (choices_selected) color by variable (subject level), None corresponds to NULL
bar_color_opt: aesthetic values to map color values (named vector to map color values to each name). If not NULL, please make sure this contains all possible values for bar_color_var values, otherwise color will be assigned by ggplot default, please note that NULL needs to be specified in this case
sort_var: (choices_selected) sort by variable (subject level), None corresponds to NULL
add_label_var_sl: (choices_selected) add label to bars (subject level), None corresponds to NULL
add_label_paramcd_rs: (choices_selected) add label to bars (response dataset), None corresponds to NULL. At least one of add_label_var_sl and add_label_paramcd_rs needs to be NULL
anno_txt_var_sl: (choices_selected) subject level variables to be displayed in the annotation table, default is NULL
anno_txt_paramcd_rs: (choices_selected) analysis dataset variables to be displayed in the annotation table, default is NULL
facet_var: (choices_selected) facet by variable (subject level), None corresponds to NULL
ytick_at: bar height axis interval, default is 20
href_line: numeric vector to plot horizontal reference lines, default is NULL
gap_point_val: singular numeric value for adding bar break when some bars are significantly higher than others, default is NULL
show_value: boolean of whether value of bar height is shown, default is TRUE
plot_height: (numeric(3))
vector to indicate default value, minimum and maximum values.
plot_width: (numeric(3))
vector to indicate default value, minimum and maximum 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.

Value

the teal::module() object.

Author

Ting Qi (qit3) qit3@gene.com

houx14 houx14@gene.com

Examples

library(nestcolor)
ADSL <- osprey::rADSL
ADRS <- osprey::rADRS
ADTR <- osprey::rADTR

ADSL$SEX <- factor(ADSL$SEX, levels = unique(ADSL$SEX))

app <- teal::init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL,
      code = "ADSL <- rADSL
              ADSL$SEX <- factor(ADSL$SEX, levels = unique(ADSL$SEX))"
    ),
    cdisc_dataset("ADRS", ADRS, code = "ADRS <- rADRS"),
    cdisc_dataset("ADTR", ADTR,
      code = " ADTR <- rADTR",
      c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
    ),
    check = TRUE
  ),
  modules = modules(
    tm_g_waterfall(
      label = "Waterfall",
      dataname_tr = "ADTR",
      dataname_rs = "ADRS",
      bar_paramcd = teal.transform::choices_selected(c("SLDINV"), "SLDINV"),
      bar_var = teal.transform::choices_selected(c("PCHG", "AVAL"), "PCHG"),
      bar_color_var = teal.transform::choices_selected(c("ARMCD", "SEX"), "ARMCD"),
      bar_color_opt = NULL,
      sort_var = teal.transform::choices_selected(c("ARMCD", "SEX"), NULL),
      add_label_var_sl = teal.transform::choices_selected(c("SEX", "EOSDY"), NULL),
      add_label_paramcd_rs = teal.transform::choices_selected(c("BESRSPI", "OBJRSPI"), NULL),
      anno_txt_var_sl = teal.transform::choices_selected(c("SEX", "ARMCD", "BMK1", "BMK2"), NULL),
      anno_txt_paramcd_rs = teal.transform::choices_selected(c("BESRSPI", "OBJRSPI"), NULL),
      facet_var = teal.transform::choices_selected(c("SEX", "ARMCD", "STRATA1", "STRATA2"), NULL),
      href_line = "-30, 20"
    )
  )
)
#> [INFO] 2023-08-14 13:53:51.7513 pid:1120 token:[] teal.osprey Initializing tm_g_waterfall
if (interactive()) {
  shinyApp(app$ui, app$server)
}