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Teal module for the heatmap by grade

Source: R/tm_g_heat_bygrade.R
tm_g_heat_bygrade.Rd

Display the heatmap by grade as a shiny module

Usage 

tm_g_heat_bygrade(
  label,
  sl_dataname,
  ex_dataname,
  ae_dataname,
  cm_dataname = NA,
  id_var,
  visit_var,
  ongo_var,
  anno_var,
  heat_var,
  conmed_var = NULL,
  fontsize = c(5, 3, 7),
  plot_height = c(600L, 200L, 2000L),
  plot_width = 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.

sl_dataname

(character) subject level dataset name, needs to be available in the list passed to the data argument of teal::init()

ex_dataname

(character) exposures dataset name, needs to be available in the list passed to the data argument of teal::init()

ae_dataname

(character) adverse events dataset name, needs to be available in the list passed to the data argument of teal::init()

cm_dataname

(character) concomitant medications dataset name, needs to be available in the list passed to the data argument of teal::init()
specify to NA if no concomitant medications data is available

id_var

(choices_seleced) unique subject ID variable

visit_var

(choices_seleced) analysis visit variable

ongo_var

(choices_seleced) study ongoing status variable. This variable is a derived logical variable. Usually it can be derived from EOSSTT.

anno_var

(choices_seleced) annotation variable

heat_var

(choices_seleced) heatmap variable

conmed_var

(choices_seleced) concomitant medications variable, specify to NA if no concomitant medications data is available

fontsize

(numeric(1) or numeric(3))
Defines initial possible range of font-size. fontsize is set for teal.widgets::optionalSliderInputValMinMax() which controls font-size in the output plot.

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.

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:

Examples 

data <- teal_data() %>%
  within({
    library(dplyr)
    library(nestcolor)
    ADSL <- rADSL %>% slice(1:30)
    ADEX <- rADEX %>% filter(USUBJID %in% ADSL$USUBJID)
    ADAE <- rADAE %>% filter(USUBJID %in% ADSL$USUBJID)
    ADCM <- rADCM %>% filter(USUBJID %in% ADSL$USUBJID)
    # This preprocess is only to force legacy standard on ADCM
    ADCM <- ADCM %>%
      select(-starts_with("ATC")) %>%
      unique()
    # function to derive AVISIT from ADEX
    .add_visit <- function(data_need_visit) {
      visit_dates <- ADEX %>%
        filter(PARAMCD == "DOSE") %>%
        distinct(USUBJID, AVISIT, ASTDTM) %>%
        group_by(USUBJID) %>%
        arrange(ASTDTM) %>%
        mutate(next_vis = lead(ASTDTM), is_last = ifelse(is.na(next_vis), TRUE, FALSE)) %>%
        rename(this_vis = ASTDTM)
      data_visit <- data_need_visit %>%
        select(USUBJID, ASTDTM) %>%
        left_join(visit_dates, by = "USUBJID") %>%
        filter(ASTDTM > this_vis & (ASTDTM < next_vis | is_last == TRUE)) %>%
        left_join(data_need_visit) %>%
        distinct()
      return(data_visit)
    }
    # derive AVISIT for ADAE and ADCM
    ADAE <- .add_visit(ADAE)
    ADCM <- .add_visit(ADCM)
    # derive ongoing status variable for ADEX
    ADEX <- ADEX %>%
      filter(PARCAT1 == "INDIVIDUAL") %>%
      mutate(ongo_status = (EOSSTT == "ONGOING"))
  })

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

ADCM <- data[["ADCM"]]

app <- init(
  data = data,
  modules = modules(
    tm_g_heat_bygrade(
      label = "Heatmap by grade",
      sl_dataname = "ADSL",
      ex_dataname = "ADEX",
      ae_dataname = "ADAE",
      cm_dataname = "ADCM",
      id_var = choices_selected(
        selected = "USUBJID",
        choices = c("USUBJID", "SUBJID")
      ),
      visit_var = choices_selected(
        selected = "AVISIT",
        choices = c("AVISIT")
      ),
      ongo_var = choices_selected(
        selected = "ongo_status",
        choices = c("ongo_status")
      ),
      anno_var = choices_selected(
        selected = c("SEX", "COUNTRY"),
        choices = c("SEX", "COUNTRY", "USUBJID")
      ),
      heat_var = choices_selected(
        selected = "AETOXGR",
        choices = c("AETOXGR")
      ),
      conmed_var = choices_selected(
        selected = "CMDECOD",
        choices = c("CMDECOD")
      ),
      plot_height = c(600, 200, 2000)
    )
  )
)
#> Initializing tm_g_heat_bygrade
if (interactive()) {
  shinyApp(app$ui, app$server)
}