fda-fig_02.R

#' FDA Figure 2: Time to Last Follow Up, Safety Population, Pooled Analyses
#'
#' @details
#' * `df` must contain the variables specified by `arm_var`, `id_var`, `saffl_var`, and `eosdy_var`.
#' * Flag variables (i.e. `XXXFL`) are expected to have two levels: `"Y"` (true) and `"N"` (false). Missing values in
#'   flag variables are treated as `"N"`.
#' * It is assumed that every record for a unique patient in `df` has the same last recorded (relative) study day.
#' * Values in the "Number of Patients" table are the number of patients for each arm with treatment duration equal to
#'   or greater than the given time (times corresponding to the figure's x-ticks labels).
#' * Records with missing treatment start and/or end datetime are excluded from all calculations.
#'
#' @inheritParams argument_convention
#' @param add_table (`flag`)\cr whether "Number of Patients" table should be printed under the plot.
#' @param annotations (named `list` of `character`)\cr list of annotations to add to the figure. Valid annotation types
#'   are `title`, `subtitles`, and `caption`. Each name-value pair should use the annotation type as name and the
#'   desired string as value.
#'
#' @return A `ggplot2` object.
#'
#' @examples
#' adsl <- random.cdisc.data::cadsl
#' adsl$EOSDY <- sample(0:400, nrow(adsl), replace = TRUE)
#'
#' fig <- make_fig_02(df = adsl)
#' fig
#'
#' @export
make_fig_02 <- function(df,
                        arm_var = "ARM",
                        id_var = "USUBJID",
                        saffl_var = "SAFFL",
                        eosdy_var = "EOSDY",
                        u_trtdur = "days",
                        x_lab = paste0("Time from first dose (", u_trtdur, ")"),
                        y_lab = "Percent of Patients (%)",
                        xticks = NA,
                        ggtheme = NULL,
                        add_table = TRUE,
                        annotations = NULL) {
  assert_subset(c(arm_var, id_var, saffl_var, eosdy_var), names(df))
  assert_choice(u_trtdur, c("days", "weeks", "months", "years"))
  assert_flag_variables(df, saffl_var)

  df <- df %>%
    filter(.data[[saffl_var]] == "Y") %>%
    df_explicit_na() %>%
    mutate(
      TLSTFU = lubridate::days(.data[[eosdy_var]]),
      TLSTFU = TLSTFU %>% as.numeric(u_trtdur),
      AVALU = u_trtdur
    ) %>%
    filter(!is.na(TLSTFU)) %>%
    select(all_of(c(id_var, arm_var)), TLSTFU) %>%
    distinct() %>%
    arrange(desc(TLSTFU))

  df$PT_PCT <- seq_len(nrow(df)) / nrow(df) * 100
  max_time <- max(df$TLSTFU)

  g <- ggplot(data = df, aes(x = TLSTFU, y = PT_PCT, group = .data[[arm_var]], color = .data[[arm_var]])) +
    geom_line() +
    labs(
      title = annotations[["title"]],
      subtitle = annotations[["subtitles"]],
      caption = annotations[["caption"]],
      x = x_lab,
      y = y_lab
    ) +
    theme(
      legend.position = "bottom",
      legend.title = element_blank(),
      plot.margin = unit(c(0.05, 0.05, 0, 0.025), "npc")
    )

  if (any(!is.na(xticks))) {
    g <- g +
      scale_x_continuous(breaks = xticks, limits = c(min(xticks), max(c(xticks, max_time))))
  }

  if (!is.null(ggtheme)) g <- g + ggtheme

  if (add_table) {
    # following 2 lines replace `g_legend <- cowplot::get_legend(g)` which is currently broken
    legend_pos <- paste0("guide-box-", ifelse(is.null(ggtheme), "bottom", ggtheme$legend.position))
    g_legend <- cowplot::get_plot_component(g, legend_pos, return_all = TRUE)

    g <- g + theme(legend.position = "none")

    xtick_lbls <- ggplot_build(g)$layout$panel_params[[1]]$x$breaks
    xtick_lbls <- xtick_lbls[!is.na(xtick_lbls)]
    xlims <- ggplot_build(g)$layout$panel_params[[1]]$x$limits

    tbl_n <- expand.grid(
      x = xtick_lbls,
      arm = rev(levels(df[[arm_var]])),
      n = 0
    )

    g_tbl <- ggplot(tbl_n, aes(x = x, y = arm)) +
      theme(
        axis.title.x = element_blank(),
        axis.title.y = element_blank(),
        axis.ticks.x = element_blank(),
        axis.ticks.y = element_blank(),
        panel.background = element_blank(),
        axis.text.x = element_blank(),
        panel.border = element_rect(color = "black", fill = NA, linewidth = 0.5),
        plot.margin = unit(c(0.1, 0.05, 0, 0.025), "npc")
      ) +
      labs(title = "Number of Patients") +
      scale_x_continuous(breaks = xtick_lbls, limits = c(min(xlims, xtick_lbls), max(xlims, xtick_lbls)))

    for (i in seq_len(nrow(tbl_n))) {
      tbl_n$n[i] <- sum(df$ARM == tbl_n$arm[i] & df$TLSTFU >= tbl_n$x[i])
      g_tbl <- g_tbl +
        annotate("text", label = as.character(tbl_n$n[i]), x = tbl_n$x[i], y = tbl_n$arm[i])
    }

    if (!is.null(ggtheme)) g_tbl <- g_tbl + ggtheme

    cowplot::plot_grid(
      g,
      g_tbl,
      g_legend,
      align = "v",
      axis = "l",
      ncol = 1,
      rel_heights = c(0.7, 0.25, 0.1)
    )
  } else {
    g
  }
}