app.R

library(scda)
library(scda.2022)
library(dplyr)
library(teal.modules.clinical)
library(teal.modules.general)
library(teal.osprey)
library(nestcolor)
# optional libraries
library(sparkline)

options(shiny.useragg = FALSE)

ADSL <- synthetic_cdisc_data("latest")$adsl

# derive ADSL treatment duration
adsl_labels <- formatters::var_labels(ADSL, fill = FALSE)
ADSL <- ADSL %>%
  mutate(
    TRTDURD = as.numeric(as.Date(TRTEDTM) - as.Date(TRTSDTM)) + 1,
    DTHFL = ifelse(!is.na(DTHDT), "Y", NA),
    EOSSTT = factor(EOSSTT, levels = c("COMPLETED", "ONGOING", "DISCONTINUED"))
  ) %>%
  formatters::var_relabel(
    TRTDURD = "Treatment Duration in Days",
    DTHFL = "Death Flag",
    DCSREAS = "Reason for Study Discontinuation",
    EOSSTT = "End of Study Status"
  ) %>%
  droplevels()
formatters::var_labels(ADSL)[c(names(adsl_labels))] <- adsl_labels

ADAE <- synthetic_cdisc_data("latest")$adae

# derive common flags for AEs
adae_labels <- formatters::var_labels(ADAE, fill = FALSE)
ADAE <- ADAE %>%
  mutate_at(c("AESOC", "AEBODSYS", "AEHLT", "AEDECOD", "AETERM", "AELLT"), as.character) %>%
  mutate(
    RELFL = ifelse(AEREL == "Y", "Y", "N"),
    CTC35FL = ifelse(AETOXGR %in% c("3", "4", "5"), "Y", "N"),
    SERFL = ifelse(AESER == "Y", "Y", "N"),
    RELSERFL = ifelse(AEREL == "Y" & AESER == "Y", "Y", "N"),
    AEREL1 = (AEREL == "Y" & ACTARM == "A: Drug X"),
    AEREL2 = (AEREL == "Y" & ACTARM == "B: Placebo"),
    ASTDT = as.Date(ASTDTM),
    AENDT = as.Date(AENDTM)
  ) %>%
  formatters::var_relabel(
    RELFL = "Related AE",
    CTC35FL = "Grade >=3 AE",
    SERFL = "Serious AE",
    RELSERFL = "Related Serious AE",
    AEREL1 = "AE related to A: Drug X",
    AEREL2 = "AE related to B: Placebo",
    ASTDT = "Analysis Start Date",
    AENDT = "Analysis End Date",
    AESOC = "Primary System Organ Class",
    AEBODSYS = "Body System or Organ Class",
    AEHLT = "High Level Term",
    AEDECOD = "Dictionary-Derived Term",
    AETERM = "Reported Term for the Adverse Event",
    AELLT = "Lowest Level Term"
  )

ADCM <- synthetic_cdisc_data("latest")$adcm

# process ADCM
ADCM <- ADCM %>%
  mutate(
    ASTDT = as.Date(ASTDTM),
    AENDT = as.Date(AENDTM)
  ) %>%
  formatters::var_relabel(
    ASTDT = "Analysis Start Date",
    AENDT = "Analysis End Date"
  )

ADEX <- synthetic_cdisc_data("latest")$adex

# process ADEX
ADEX <- ADEX %>%
  mutate(
    ASTDT = as.Date(ASTDTM),
    AENDT = as.Date(AENDTM)
  ) %>%
  formatters::var_relabel(
    ASTDT = "Analysis Start Date",
    AENDT = "Analysis End Date"
  )

ADTR <- synthetic_cdisc_data("latest")$adtr

# process ADTR
adtr_labels <- formatters::var_labels(ADTR, fill = FALSE)
ADTR <- ADTR %>%
  mutate(
    PCHG = ifelse(AVISIT == "BASELINE", 0, PCHG),
    CHG = ifelse(AVISIT == "BASELINE", 0, CHG),
    AVAL = ifelse(AVISIT == "BASELINE", BASE, AVAL),
    AVALC = ifelse(AVISIT == "BASELINE", as.character(BASE), AVALC)
  ) %>%
  filter(AVISIT != "SCREENING")
formatters::var_labels(ADTR) <- adtr_labels

ADTRWF <- ADTR %>%
  filter(AVISIT != "BASELINE")
formatters::var_labels(ADTRWF) <- formatters::var_labels(ADTR, fill = FALSE)


# process ADRS
ADRSSWIM <- synthetic_cdisc_data("latest")$adrs %>%
  filter(PARAMCD == "OVRINV") %>%
  arrange(USUBJID)

ADRS <- synthetic_cdisc_data("latest")$adrs
adrs_labels <- formatters::var_labels(ADRS, fill = FALSE)
ADRS <- ADRS %>%
  filter(PARAMCD %in% c("BESRSPI", "INVET")) %>%
  mutate(ADT = as.Date(ADTM)) %>%
  droplevels()
formatters::var_labels(ADRS) <- c(adrs_labels, "Analysis Date")

ADLB <- synthetic_cdisc_data("latest")$adlb

# process ADLB
ADLB <- ADLB %>%
  mutate(
    ADT = as.Date(ADTM),
    LBSTRESN = as.numeric(LBSTRESC)
  ) %>%
  formatters::var_relabel(
    ADT = "Analysis Date",
    LBSTRESN = "Numeric Result/Finding in Standard Units"
  )

## Reusable Configuration For Modules
arm_vars <- c("ARMCD", "ARM", "ACTARMCD", "ACTARM", "EOSSTT")
aeflag_vars <- c("RELFL", "CTC35FL", "SERFL", "RELSERFL")
facet_vars <- c("SEX", "BMRKR2", "RACE", "STRATA1", "STRATA2")
ds_vars <- c("EOSSTT", "DCSREAS")

cs_arm_var <- choices_selected(
  choices = variable_choices(ADSL, subset = arm_vars),
  selected = "ARM"
)

cs_aeflag_var <- choices_selected(
  choices = variable_choices(ADAE, subset = aeflag_vars),
  selected = NULL
)

cs_aeterm_var <- choices_selected(
  choices = variable_choices(ADAE, subset = c("AEDECOD", "AETERM", "AELLT", "AESOC", "AEBODSYS", "AEHLT")),
  selected = "AEDECOD"
)

cs_facet_var <- choices_selected(
  choices = variable_choices(ADSL, subset = facet_vars),
  selected = NULL
)

cs_ds_var <- choices_selected(
  choices = variable_choices(ADSL, ds_vars),
  selected = ds_vars
)

cs_bar_var <- choices_selected(
  choices = variable_choices(ADSL, c("TRTDURD", "EOSDY")),
  selected = "TRTDURD"
)

cs_paramcd_rsp <- choices_selected(
  choices = value_choices(ADRS, "PARAMCD", "PARAM", subset = c("BESRSPI", "INVET")),
  selected = "BESRSPI"
)

cs_paramcd_tr <- choices_selected(
  choices = value_choices(ADTR, "PARAMCD", "PARAM", subset = "SLDINV"),
  selected = "SLDINV"
)

adsl_labels <- formatters::var_labels(ADSL)
fact_vars_asl <- names(Filter(isTRUE, sapply(ADSL, is.factor)))

date_vars_asl <- names(ADSL)[vapply(ADSL, function(x) inherits(x, c("Date", "POSIXct", "POSIXlt")), logical(1))]
demog_vars_asl <- names(ADSL)[!(names(ADSL) %in% c("USUBJID", "STUDYID", date_vars_asl))]

## Create front page for app ----
srv_front_page <- function(id, datasets, dataname) {
  moduleServer(id, function(input, output, session) {
    observeEvent(input$show_teal_setup_code, {
      showModal(modalDialog(
        title = "R Code Used to Setup the Current Teal Shiny App",
        tags$div(
          actionButton("copyRCode", "Copy to Clipboard", `data-clipboard-target` = "#r_code"),
          style = "padding-bottom: 15px;"
        ),
        tags$div(tags$pre(id = "r_code", paste(readLines("app.R"), collapse = "\n"))),
        footer = tagList(
          actionButton("copyRCode", "Copy to Clipboard", `data-clipboard-target` = "#r_code"),
          modalButton("Dismiss")
        ),
        size = "l",
        easyClose = TRUE
      ))
    })
  })
}

ui_front_page <- function(id, ...) {
  ns <- NS(id)
  tagList(
    tags$p(
      "The", tags$code("ADSL"), ",", tags$code("ADAE"), ",", tags$code("ADRS"), ", and ",
      tags$code("ADTR"), "data in this example app has been created using random number generators."
    ),
    tags$p("", style = "height: 20px;"),
    tags$p(
      "This sample app mainly covers ", tags$code("teal.osprey"), " modules.",
      "If additional safety and efficacy modules are needed,",
      "please refer to the safety and efficacy sample app templates",
      "to add additional modules."
    ),
    tags$p("", style = "height: 15px;"),
    tags$p(paste(
      "These apps are relatively easily setup for a study.",
      "That is, the teal framework is optimized to setup one",
      "Shiny App per analysis purpose. For example, the code to setup",
      "the current teal app can be requested with the following button:"
    )),
    tags$p("", style = "height: 15px;"),
    actionButton(ns("show_teal_setup_code"), "Show Teal Shiny App Setup R-Code", icon = icon("fas fa-align-justify")),
    tags$p("", style = "height: 20px;"),
    tags$div(
      tags$p(
        "This is shiny app was brought to you by ED SPA. For more information please contact NEST SME team."
      )
    )
  )
}

# create cdisc_dataset objects to pass into app

adsl <- cdisc_dataset(
  dataname = "ADSL",
  x = ADSL,
  code = 'ADSL <- synthetic_cdisc_data("latest")$adsl
          adsl_labels <- formatters::var_labels(ADSL, fill = FALSE)
          ADSL <- ADSL %>%
              mutate(
                TRTDURD = as.numeric(as.Date(TRTEDTM) - as.Date(TRTSDTM)) + 1,
                DTHFL = ifelse(!is.na(DTHDT), "Y", NA),
                EOSSTT = factor(EOSSTT, levels = c("COMPLETED", "ONGOING", "DISCONTINUED"))
              ) %>%
              formatters::var_relabel(
                TRTDURD = "Treatment Duration in Days",
                DTHFL = "Death Flag",
                DCSREAS = "Reason for Study Discontinuation",
                EOSSTT = "End of Study Status"
              ) %>%
              droplevels()
          formatters::var_labels(ADSL)[c(names(adsl_labels))] <- adsl_labels'
)

adae <- cdisc_dataset(
  dataname = "ADAE",
  x = ADAE,
  keys = c("STUDYID", "USUBJID", "AETERM", "AESEQ"),
  code = 'ADAE <- synthetic_cdisc_data("latest")$adae
          # derive common flags for AEs
          ADAE <- ADAE %>%
            mutate_at(
              c("AESOC", "AEBODSYS", "AEHLT", "AEDECOD", "AETERM", "AELLT"),
              as.character
            ) %>%
            mutate(
              RELFL = ifelse(AEREL == "Y", "Y", "N"),
              CTC35FL = ifelse(AETOXGR %in% c("3", "4", "5"), "Y", "N"),
              SERFL = ifelse(AESER == "Y", "Y", "N"),
              RELSERFL = ifelse(AEREL == "Y" & AESER == "Y", "Y", "N"),
              AEREL1 = (AEREL == "Y" & ACTARM == "A: Drug X"),
              AEREL2 = (AEREL == "Y" & ACTARM == "B: Placebo"),
              ASTDT = as.Date(ASTDTM),
              AENDT = as.Date(AENDTM)
            ) %>%
            formatters::var_relabel(
              RELFL = "Related AE",
              CTC35FL = "Grade >=3 AE",
              SERFL = "Serious AE",
              RELSERFL = "Related Serious AE",
              AEREL1 = "AE related to A: Drug X",
              AEREL2 = "AE related to B: Placebo",
              ASTDT = "Analysis Start Date",
              AENDT = "Analysis End Date",
              AESOC = "Primary System Organ Class",
              AEBODSYS = "Body System or Organ Class",
              AEHLT = "High Level Term",
              AEDECOD = "Dictionary-Derived Term",
              AETERM = "Reported Term for the Adverse Event",
              AELLT = "Lowest Level Term"
            )',
  vars = list(ADSL = adsl)
)

adcm <- cdisc_dataset(
  dataname = "ADCM",
  x = ADCM,
  code = 'ADCM <- synthetic_cdisc_data("latest")$adcm
          ADCM <- ADCM %>%
            mutate(
              ASTDT = as.Date(ASTDTM),
              AENDT = as.Date(AENDTM)
            ) %>%
            formatters::var_relabel(
              ASTDT = "Analysis Start Date",
              AENDT = "Analysis End Date"
            )',
  vars = list(ADSL = adsl)
)

adex <- cdisc_dataset(
  dataname = "ADEX",
  x = ADEX,
  code = 'ADEX <- synthetic_cdisc_data("latest")$adex
          ADEX <- ADEX %>%
            mutate(
              ASTDT = as.Date(ASTDTM),
              AENDT = as.Date(AENDTM)
            ) %>%
            formatters::var_relabel(
              ASTDT = "Analysis Start Date",
              AENDT = "Analysis End Date"
            )',
  vars = list(ADSL = adsl)
)

adtr <- cdisc_dataset(
  dataname = "ADTR",
  x = ADTR,
  keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
  code = 'ADTR <- synthetic_cdisc_data("latest")$adtr
          adtr_labels <- formatters::var_labels(ADTR, fill = FALSE)
          ADTR <- ADTR %>%
            mutate(
              PCHG = ifelse(AVISIT == "BASELINE", 0, PCHG),
              CHG = ifelse(AVISIT == "BASELINE", 0, CHG),
              AVAL = ifelse(AVISIT == "BASELINE", BASE, AVAL),
              AVALC = ifelse(AVISIT == "BASELINE", as.character(BASE), AVALC)
            ) %>%
            dplyr::filter(AVISIT != "SCREENING")
          formatters::var_labels(ADTR) <- adtr_labels',
  var = list(ADSL = adsl)
)

adtrwf <- cdisc_dataset(
  dataname = "ADTRWF",
  x = ADTRWF,
  keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
  code = 'ADTRWF <- ADTR %>%
            dplyr::filter(AVISIT != "BASELINE")
          formatters::var_labels(ADTRWF) <- formatters::var_labels(ADTR, fill = FALSE)',
  vars = list(ADTR = adtr)
)

adrs <- cdisc_dataset(
  dataname = "ADRS",
  x = ADRS,
  code = 'ADRS <- synthetic_cdisc_data("latest")$adrs
          adrs_labels <- formatters::var_labels(ADRS, fill = FALSE)
          ADRS <- ADRS %>%
            filter(PARAMCD %in% c("BESRSPI", "INVET"))  %>%
            mutate(ADT = as.Date(ADTM)) %>%
            droplevels()
        formatters::var_labels(ADRS) <- c(adrs_labels, "Analysis Date")',
  vars = list(ADSL = adsl)
)

adrsswim <- cdisc_dataset(
  dataname = "ADRSSWIM",
  x = ADRSSWIM,
  keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
  code = 'ADRSSWIM <- synthetic_cdisc_data("latest")$adrs %>%
            dplyr::filter(PARAMCD == "OVRINV") %>%
            arrange(USUBJID)',
  vars = list(ADSL = adsl)
)

adlb <- cdisc_dataset(
  dataname = "ADLB",
  x = ADLB,
  code = 'ADLB <- synthetic_cdisc_data("latest")$adlb
          ADLB <- ADLB %>%
            mutate(
              ADT = as.Date(ADTM),
              LBSTRESN = as.numeric(LBSTRESC)
            ) %>%
            formatters::var_relabel(
              ADT = "Analysis Date",
              LBSTRESN = "Numeric Result/Finding in Standard Units"
            )',
  vars = list(ADSL = adsl)
)

## Setup App
app <- teal::init(
  data = cdisc_data(
    adsl,
    adae,
    adex,
    adcm,
    adtr,
    adtrwf,
    adrs,
    adrsswim,
    adlb,
    check = TRUE
  ),
  modules = modules(
    module(
      label = "App Information",
      server = srv_front_page,
      ui = ui_front_page,
      filters = "all"
    ),
    tm_data_table("Data Table"),
    tm_variable_browser("Variable Browser"),
    modules(
      label = "Adverse Events",
      tm_g_events_term_id(
        label = "Common AE Plot",
        dataname = "ADAE",
        term_var = cs_aeterm_var,
        arm_var = cs_arm_var,
        plot_height = c(800, 200, 2000)
      ),
      tm_g_ae_oview(
        label = "AE Overview Plot",
        dataname = "ADAE",
        arm_var = cs_arm_var,
        flag_var_anl = choices_selected(
          choices = variable_choices(ADAE, c("AEREL1", "AEREL2")),
          selected = NULL
        ),
        plot_height = c(800, 200, 2000)
      ),
      tm_g_butterfly(
        label = "Butterfly Plot",
        dataname = "ADAE",
        filter_var = cs_aeflag_var,
        right_var = cs_arm_var,
        left_var = cs_arm_var,
        category_var = choices_selected(
          choices = variable_choices(ADAE, subset = c("AEDECOD", "AETERM", "AESOC", "AEBODSYS")),
          selected = "AEBODSYS"
        ),
        color_by_var = choices_selected(
          choices = c(variable_choices(ADAE, "AETOXGR"), "None"),
          selected = "AETOXGR"
        ),
        count_by_var = choices_selected(
          choices = c("# of patients", "# of AEs"),
          selected = "# of patients"
        ),
        facet_var = cs_facet_var,
        sort_by_var = choices_selected(choices = c("count", "alphabetical"), selected = "count"),
        legend_on = TRUE,
        plot_height = c(600, 200, 2000)
      ),
      tm_g_ae_sub(
        label = "AE by Subgroup",
        dataname = "ADAE",
        arm_var = choices_selected(
          selected = "ACTARMCD",
          choices = c("ACTARM", "ACTARMCD")
        ),
        group_var = choices_selected(
          selected = c("SEX", "REGION1", "RACE"),
          choices = c("SEX", "REGION1", "RACE")
        ),
        plot_height = c(600, 200, 2000)
      )
    ),
    tm_t_summary(
      label = "Disposition Table",
      dataname = "ADSL",
      arm_var = cs_arm_var,
      summarize_vars = cs_ds_var,
      useNA = "no"
    ),
    tm_g_spiderplot(
      label = "Spider plot",
      dataname = "ADTR",
      paramcd = cs_paramcd_tr,
      x_var = choices_selected(choices = variable_choices(ADTR, "ADY"), selected = "ADY"),
      y_var = choices_selected(
        choices = variable_choices(ADTR, c("PCHG", "CHG", "AVAL")),
        selected = "PCHG"
      ),
      marker_var = choices_selected(
        choices = variable_choices(ADSL, c("SEX", "RACE")),
        selected = "SEX"
      ),
      line_colorby_var = cs_arm_var,
      xfacet_var = cs_facet_var,
      yfacet_var = cs_facet_var,
      vref_line = "42",
      href_line = "-20, 0, 30",
      anno_txt_var = TRUE,
      legend_on = FALSE,
      plot_height = c(600, 200, 2000)
    ),
    tm_g_swimlane(
      label = "Swimlane Plot",
      dataname = "ADRSSWIM",
      bar_var = cs_bar_var,
      bar_color_var = choices_selected(
        choices = variable_choices(ADSL, fact_vars_asl),
        selected = "EOSSTT"
      ),
      sort_var = choices_selected(
        choices = variable_choices(ADSL, c(arm_vars, "TRTDURD")),
        selected = arm_vars[1]
      ),
      marker_pos_var = choices_selected(
        choices = c(variable_choices(ADRS, "ADY")),
        selected = "ADY"
      ),
      marker_shape_var = choices_selected(c(variable_choices(ADRS, c("AVALC", "AVISIT"))),
        selected = "AVALC"
      ),
      marker_shape_opt = c("CR" = 16, "PR" = 17, "SD" = 18, "PD" = 15, "Death" = 8),
      marker_color_var = choices_selected(
        choices = c(variable_choices(ADRS, c("AVALC", "AVISIT"))),
        selected = "AVALC"
      ),
      marker_color_opt = c(
        "CR" = "green", "PR" = "blue", "SD" = "goldenrod",
        "PD" = "red", "Death" = "black"
      ),
      vref_line = c(30, 60),
      anno_txt_var = choices_selected(
        choices = variable_choices(ADSL, intersect(arm_vars, fact_vars_asl)),
        selected = arm_vars[1]
      )
    ),
    tm_g_waterfall(
      label = "Waterfall Plot",
      dataname_tr = "ADTRWF",
      dataname_rs = "ADRS",
      bar_paramcd = cs_paramcd_tr,
      bar_var = choices_selected(variable_choices(ADTRWF, "PCHG"), "PCHG"),
      bar_color_var = choices_selected(variable_choices(ADSL, fact_vars_asl), "ARMCD"),
      sort_var = choices_selected(variable_choices(ADSL, fact_vars_asl), NULL),
      add_label_var_sl = choices_selected(variable_choices(ADSL, fact_vars_asl), NULL),
      add_label_paramcd_rs = cs_paramcd_rsp,
      anno_txt_var_sl = choices_selected(variable_choices(ADSL, fact_vars_asl), NULL),
      anno_txt_paramcd_rs = cs_paramcd_rsp,
      facet_var = cs_facet_var,
      ytick_at = 20,
      href_line = "-30, 20",
      gap_point_val = NULL,
      plot_height = c(1200L, 400L, 5000L)
    ),
    tm_g_patient_profile(
      label = "Patient Profile Plot",
      patient_id = choices_selected(
        choices = unique(ADSL$USUBJID),
        selected = unique(ADSL$USUBJID)[1]
      ),
      sl_dataname = "ADSL",
      ex_dataname = "ADEX",
      ae_dataname = "ADAE",
      rs_dataname = "ADRS",
      cm_dataname = "ADCM",
      lb_dataname = "ADLB",
      sl_start_date = choices_selected(
        selected = "TRTSDTM",
        choices = variable_choices(ADSL, subset = c("TRTSDTM", "RANDDT"))
      ),
      ex_var = choices_selected(
        selected = "PARCAT2",
        choices = variable_choices(ADEX, "PARCAT2")
      ),
      ae_var = choices_selected(
        selected = "AEDECOD",
        choices = variable_choices(ADAE, c("AEDECOD", "AESOC"))
      ),
      ae_line_col_var = choices_selected(
        selected = "AESER",
        choices = variable_choices(ADAE, c("AESER", "AEREL"))
      ),
      ae_line_col_opt = c("Y" = "red", "N" = "blue"),
      rs_var = choices_selected(
        selected = "PARAMCD",
        choices = variable_choices(ADRS, c("PARAMCD", "PARAM"))
      ),
      cm_var = choices_selected(
        selected = "CMDECOD",
        choices = variable_choices(ADCM, c("CMDECOD", "CMCAT"))
      ),
      lb_var = choices_selected(
        selected = "PARAMCD",
        choices = variable_choices(ADLB, c("PARAMCD", "PARAM"))
      ),
      x_limit = "-28, 750",
      plot_height = c(1200, 400, 5000)
    )
  ),
  header = div(
    class = "",
    style = "margin-bottom: 2px;",
    tags$h1("Demo ED Onco teal app with random ADaM data", tags$span("ED SPA", class = "pull-right"))
  ),
  footer = tags$p(class = "text-muted", "Source: teal.gallery package")
)

## Start Teal Shiny App ----
shinyApp(app$ui, app$server)