Create vx_line_plot.R

R/vx_line_plot.R

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+# Copyright 2024 Pfizer Inc
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+#' Pre-Process data for Line Plot
+#'
+#' @inheritParams process_vx_scatter_data
+#'
+#' @return Dataframe containing analysis values for requisite vaccine line plot statistics
+#' @export
+#'
+#' @examples
+#' data("vx_line_data")
+#'
+#' process_line_plot_data(
+#'   dataset_adsl = vx_line_data$adsl,
+#'   dataset_analysis = vx_line_data$adva,
+#'   adsl_subset = "SAFFL == 'Y'",
+#'   analysis_subset = 'PARAMN==2 & TRTARN!=""& (AVISITN %in% c(1,3,4,5,6,7))',
+#'   split_by = "SEX",
+#'   trtvar = "TRTP",
+#'   trtsort = "TRTPN",
+#'   xvar = "AVISIT",
+#'   yvar = "AVAL"
+#' )
+#'
+process_line_plot_data <-
+  function(dataset_adsl,
+           dataset_analysis,
+           adsl_subset,
+           analysis_subset,
+           split_by = NA_character_,
+           trtvar,
+           trtsort,
+           xvar = "AVISIT",
+           yvar = "AVAL",
+           legendbign = "Y") {
+    # Checking if datasets are empty or not
+    stopifnot("ADSL data is empty" = nrow(dataset_adsl) != 0)
+    stopifnot("Analysis data is empty" = nrow(dataset_analysis) != 0)
+
+    if (!is.na(split_by) && str_squish(split_by) != "") {
+      stopifnot(all(str_to_vec(split_by) %in% toupper(names(dataset_adsl))))
+    }
+
+    # Merge with adsl
+    adsl_merged <- adsl_merge(
+      dataset_adsl,
+      adsl_subset,
+      dataset_analysis
+    ) |>
+      mentry(
+        subset = analysis_subset,
+        trtvar = trtvar,
+        trtsort = trtsort,
+        byvar = xvar,
+        subgrpvar = str_remove_all(split_by, " "),
+        trttotalyn = "N",
+        sgtotalyn = "N",
+        add_grpmiss = "N",
+        pop_fil = NA
+      )
+    # Creating the final dataset
+    final_data <- adsl_merged |>
+      msumstat(
+        dptvar = yvar,
+        statvar = "geommean~geom_lowci~geom_upci",
+        sigdec = 2,
+        dptvarn = 1
+      )
+    # N count for graph output and prep for graph
+    plot_data <- plot_title_nsubj(
+      adsl_merged,
+      final_data[["gsum"]],
+      var_start(final_data[["gsum"]], "SUBGRP")
+    ) |>
+      mutate(
+        across(all_of(c("geommean", "geom_lowci", "geom_upci")), as.numeric),
+        XVAR = fct_reorder(str_to_title(.data[["BYVAR1"]]), .data[["BYVAR1N"]]),
+        YVAR = .data[["geommean"]]
+      ) |>
+      plot_display_bign(mentry_data = adsl_merged, bignyn = legendbign)
+    return(plot_data)
+  }
+
+#' Utility for Vaccine Line Plot - (Line Plot with error limits).
+#' @inheritParams line_plot
+#'
+#' @return plot_vx -> Vaccine Line Plot
+#' @export
+#'
+#' @examples
+#' data("vx_line_data")
+#'
+#' lineplot_df <- process_line_plot_data(
+#'   dataset_adsl = vx_line_data$adsl,
+#'   dataset_analysis = vx_line_data$adva,
+#'   adsl_subset = "SAFFL == 'Y'",
+#'   analysis_subset = 'PARAMN==2 & TRTARN!=""& (AVISITN %in% c(1,3,4,5,6,7))',
+#'   trtvar = "TRTP",
+#'   trtsort = "TRTPN",
+#'   xvar = "AVISIT",
+#'   yvar = "AVAL"
+#' )
+#'
+#' vx_plot <- vx_line_plot(
+#'   datain = lineplot_df,
+#'   series_opts = list(color = g_seriescol(lineplot_df, NA, "TRTVAR")),
+#'   axis_opts = plot_axis_opts(
+#'     ylinearopts = list(
+#'       breaks = c(100, 1000, 10000, 100000),
+#'       limits = c(100, 100000)
+#'     ),
+#'     xaxis_label = "Visit",
+#'     yaxis_label = "Geometric Mean Titer",
+#'     yaxis_scale = "log10"
+#'   ),
+#'   legend_opts = list(
+#'     label = "",
+#'     pos = "bottom",
+#'     dir = "horizontal"
+#'   ),
+#'   griddisplay = "N"
+#' )
+#'
+#' vx_plot
+#'
+vx_line_plot <- function(datain,
+                         axis_opts = plot_axis_opts(),
+                         series_opts,
+                         legend_opts = list(
+                           lab = "",
+                           pos = "bottom",
+                           dir = "horizontal"
+                         ),
+                         griddisplay = "N") {
+  plot_vx <- line_plot(
+    datain = datain,
+    legend_opts = legend_opts,
+    axis_opts = axis_opts,
+    series_opts = series_opts,
+    series_var = "TRTVAR",
+    series_labelvar = ifelse("TRTTXT" %in% names(datain), "TRTTXT", "TRTVAR"),
+    griddisplay = griddisplay,
+    plot_title = glue("Number of Participants N = {unique(datain$splitN)}")
+  ) +
+    geom_errorbar(aes(x = XVAR, ymin = geom_lowci, ymax = geom_upci),
+      width = .5,
+      position = position_dodge(0.03)
+    )
+  message("VX Line Plot Generated")
+  return(plot_vx)
+}