WIP variable_choices with choices as delayed_data

[m7pr]

WIP - tries to provide fixes for insightsengineering/teal.goshawk#301

Testing (dirty) with below code. Dirty because I am assigning objects to .GlobalEnv

pkgload::load_all("../teal.widgets")
pkgload::load_all(".")
data1 <- within(
  teal_data(),
  {
    ADLB <- teal.data::rADLB
    ADSL <- teal.data::rADSL
    
    library(dplyr)
    library(nestcolor)
    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"
    )
    set.seed(1)
    ADSL <- rADSL
    ADLB <- 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 = 50,
        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")
    
    assign(x = "adlb_names", value =  names(ADLB)[26:193], envir = .GlobalEnv)
    
  }
)
datanames <- c("ADLB", "ADSL")

datanames(data1) <- datanames
join_keys(data1) <- default_cdisc_join_keys[datanames]


cs_facet_var <- choices_selected(
  variable_choices("ADSL", subset = function(data){
    na.omit(c("AVISITCD", "ARM", get("adlb_names", .GlobalEnv)))
  })
)

app <- init(
  data = data1,
  modules = modules(
    tm_g_gh_boxplot(
      label = "Box Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      yaxis_var = choices_selected(c("AVAL", "BASE", "CHG"), "AVAL"),
      xaxis_var = choices_selected(c("ACTARM", "ARM", "AVISITCD", "STUDYID"), "ARM"),
      facet_var = cs_facet_var,
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      loq_legend = TRUE,
      rotate_xlab = FALSE,
      hline_arb = c(60, 55),
      hline_arb_color = c("grey", "red"),
      hline_arb_label = c("default_hori_A", "default_hori_B"),
      hline_vars = c("ANRHI", "ANRLO", "ULOQN", "LLOQN"),
      hline_vars_colors = c("pink", "brown", "purple", "black"),
    )
  ),
  title = "my teal app"
)

shinyApp(app$ui, app$server)

[gogonzo]

isn't raw_choices a function of data? I think so, which means that this change introduces a bug, as evaluation raw_choices() will throw an error

[m7pr]

this whole PR was wrong, I will write what was the fix on the original issue insightsengineering/teal.goshawk#301