bring back AVALU column for ANL dataset in correlationplot

[m7pr]

Closes #294

During this commit 66600b7 the column names used by ANL has been limited to below

66600b7#diff-c9374cc48aaf677763407e617de66326cfc22059b3c7e5875a57801162aa326cR521-R525

This PR brings back AVALU column that is used as a differentiator of the behavior of labels and title appearance for the plot.

Code to run the app (example from `?tm_g_gh_correlationplot`

# devtools::load_all(".")
# Example using ADaM structure analysis dataset.
data <- teal_data()
data <- within(data, {
  library(dplyr)
  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"
  )
  color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C")
  # assign LOQ flag symbols: circles for "N" and triangles for "Y", squares for "NA"
  shape_manual <- c("N" = 1, "Y" = 2, "NA" = 0)
  
  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",
          trimws(
            substr(
              AVISIT,
              start = 6,
              stop = str_locate(AVISIT, "DAY") - 1
            )
          )
        ),
      TRUE ~ NA_character_
    )) %>%
    mutate(AVISITCDN = case_when(
      AVISITCD == "SCR" ~ -2,
      AVISITCD == "BL" ~ 0,
      grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
      TRUE ~ NA_real_
    )) %>%
    # use ARMCD values to order treatment in visualization legend
    mutate(TRTORD = ifelse(grepl("C", ARMCD), 1,
                           ifelse(grepl("B", ARMCD), 2,
                                  ifelse(grepl("A", ARMCD), 3, NA)
                           )
    )) %>%
    mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>%
    mutate(ARM = factor(ARM) %>%
             reorder(TRTORD)) %>%
    mutate(
      ANRHI = case_when(
        PARAMCD == "ALT" ~ 60,
        PARAMCD == "CRP" ~ 70,
        PARAMCD == "IGA" ~ 80,
        TRUE ~ NA_real_
      ),
      ANRLO = case_when(
        PARAMCD == "ALT" ~ 20,
        PARAMCD == "CRP" ~ 30,
        PARAMCD == "IGA" ~ 40,
        TRUE ~ NA_real_
      )
    ) %>%
    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[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
  attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
  
  # add LLOQ and ULOQ variables
  ADLB_LOQS <- h_identify_loq_values(ADLB, "LOQFL")
  ADLB <- left_join(ADLB, ADLB_LOQS, by = "PARAM")
})

datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames

join_keys(data) <- default_cdisc_join_keys[datanames]

app <- init(
  data = data,
  modules = modules(
    tm_g_gh_correlationplot(
      label = "Correlation Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      xaxis_param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      yaxis_param = choices_selected(c("ALT", "CRP", "IGA"), "CRP"),
      xaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "BASE"),
      yaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      color_manual = c(
        "Drug X 100mg" = "#000000",
        "Placebo" = "#3498DB",
        "Combination 100mg" = "#E74C3C"
      ),
      shape_manual = c("N" = 1, "Y" = 2, "NA" = 0),
      plot_height = c(500, 200, 2000),
      facet_ncol = 2,
      visit_facet = TRUE,
      reg_line = FALSE,
      loq_legend = TRUE,
      font_size = c(12, 8, 20),
      dot_size = c(1, 1, 12),
      reg_text_size = c(3, 3, 10),
      hline_arb = c(40, 50),
      hline_arb_label = "arb hori label",
      hline_arb_color = c("red", "blue"),
      hline_vars = c("ANRHI", "ANRLO", "ULOQN", "LLOQN"),
      hline_vars_colors = c("green", "blue", "purple", "cyan"),
      hline_vars_labels = c("ANRHI Label", "ANRLO Label", "ULOQN Label", "LLOQN Label"),
      vline_vars = c("ANRHI", "ANRLO", "ULOQN", "LLOQN"),
      vline_vars_colors = c("yellow", "orange", "brown", "gold"),
      vline_vars_labels = c("ANRHI Label", "ANRLO Label", "ULOQN Label", "LLOQN Label"),
      vline_arb = c(50, 70),
      vline_arb_label = "arb vert A",
      vline_arb_color = c("green", "orange")
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

Before the PR - no unit values on the plot titles/axes

After the PR - unit values on plot titles/axes

[github-actions]

Code Coverage Summary

Filename                                 Stmts    Miss  Cover    Missing
-------------------------------------  -------  ------  -------  ---------
R/tm_g_gh_boxplot.R                        352     352  0.00%    175-594
R/tm_g_gh_correlationplot.R                555     555  0.00%    227-891
R/tm_g_gh_density_distribution_plot.R      278     278  0.00%    135-463
R/tm_g_gh_lineplot.R                       565     565  0.00%    161-820
R/tm_g_gh_scatterplot.R                    245     245  0.00%    144-441
R/tm_g_gh_spaghettiplot.R                  315     315  0.00%    194-590
R/toggleable_slider.R                      154     154  0.00%    72-243
R/utils-arbitrary_lines.r                  125     125  0.00%    19-176
R/utils-data_constraints.r                 190     190  0.00%    2-257
R/utils-keep_range_slider_updated.r         23      23  0.00%    8-38
R/utils-maptrt.r                             9       9  0.00%    24-36
R/utils-templ_ui.r                          48      48  0.00%    2-73
R/utils.R                                   49      49  0.00%    12-112
R/zzz.R                                      2       2  0.00%    2-3
TOTAL                                     2910    2910  0.00%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 728c081

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results