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Teal Module for Waterfall Plot

Source: R/tm_g_waterfall.R
tm_g_waterfall.Rd

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,
  transformators = list()
)

Arguments

label

(character(1)) Label shown in the navigation item for the module or module group. For modules() defaults to "root". See Details.

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 teal::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 teal::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.

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

the teal::module() 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:

Author

Ting Qi (qit3) qit3@gene.com

houx14 houx14@gene.com

Examples 

data <- teal_data() %>%
  within({
    library(nestcolor)
    ADSL <- rADSL
    ADRS <- rADRS
    ADTR <- rADTR
    ADSL$SEX <- factor(ADSL$SEX, levels = unique(ADSL$SEX))
  })

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

app <- init(
  data = data,
  modules = modules(
    tm_g_waterfall(
      label = "Waterfall",
      dataname_tr = "ADTR",
      dataname_rs = "ADRS",
      bar_paramcd = choices_selected(c("SLDINV"), "SLDINV"),
      bar_var = choices_selected(c("PCHG", "AVAL"), "PCHG"),
      bar_color_var = choices_selected(c("ARMCD", "SEX"), "ARMCD"),
      bar_color_opt = NULL,
      sort_var = choices_selected(c("ARMCD", "SEX"), NULL),
      add_label_var_sl = choices_selected(c("SEX", "EOSDY"), NULL),
      add_label_paramcd_rs = choices_selected(c("BESRSPI", "OBJRSPI"), NULL),
      anno_txt_var_sl = choices_selected(c("SEX", "ARMCD", "BMK1", "BMK2"), NULL),
      anno_txt_paramcd_rs = choices_selected(c("BESRSPI", "OBJRSPI"), NULL),
      facet_var = choices_selected(c("SEX", "ARMCD", "STRATA1", "STRATA2"), NULL),
      href_line = "-30, 20"
    )
  )
)
#> Initializing tm_g_waterfall
if (interactive()) {
  shinyApp(app$ui, app$server)
}