Replace GGally::ggpairs() with base graphics::pairs()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: endpoints
 Title: Simulate Correlated Multi-Endpoint Clinical Trial Data
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: 
     c(person(given = "Colin",
              family = "Longhurst",
@@ -28,13 +28,12 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
 Imports: 
-    ggplot2,
-    GGally,
     Matrix,
     MASS,
     stats,
     survival
 Suggests:
+    ggplot2,
     tidyr,
     geeM,
     lme4,

R/utils.R

@@ -1418,10 +1418,11 @@ print.summary.makeDataSim <- function(x, ...) {
 #' endpoints stored in a \code{"makeDataSim"} object returned by
 #' \code{\link{makeData}}.
 #'
-#' The method uses \code{GGally::ggpairs()} to display scatterplots in the
-#' upper triangle and pairwise correlations in the lower triangle for the
-#' selected study arm. This is intended as a quick diagnostic tool for
-#' inspecting the joint structure of simulated endpoints.
+#' The method uses \code{\link[graphics]{pairs}()} to display scatterplots
+#' in the upper triangle and Pearson correlation
+#' coefficients in the lower triangle for the selected study arm. This is
+#' intended as a quick diagnostic tool for inspecting the joint structure of
+#' simulated endpoints.
 #'
 #'
 #' @param x An object of class \code{"makeDataSim"}, created by
@@ -1441,11 +1442,9 @@ print.summary.makeDataSim <- function(x, ...) {
 #' endpoints. This affects only the displayed labels in the plot and does not
 #' modify the underlying data.
 #' @param \dots Additional arguments passed directly to
-#' \code{GGally::ggpairs()}. This can be used to customize panels, labels,
-#' sizing, or other plot options.
-#' @return A \code{GGally::ggpairs} object, which is also a
-#' \code{ggplot}-compatible object and can be printed or further modified using
-#' standard \pkg{ggplot2} syntax.
+#' \code{\link[graphics]{pairs}()}. This can be used to customize panels,
+#' labels, sizing, or other plot options.
+#' @return A base-graphics plot. Returns \code{invisible(NULL)}.
 #' @section Displayed data:
 #'
 #' The plotting method extracts the simulated endpoint columns recorded in
@@ -1456,14 +1455,11 @@ print.summary.makeDataSim <- function(x, ...) {
 #' \item{Time-to-event endpoints}{\code{TTE_1}, \code{TTE_2}, \dots} } Columns
 #' such as \code{trt}, \code{Status_*}, and \code{enrollTime} are not included
 #' in the pair plot.
-#' @section Panel layout: The returned \code{ggpairs} object is configured as
-#' follows: \itemize{ \item upper triangle: scatterplots for continuous-style
-#' panels, \item lower triangle: pairwise correlations, \item title: \code{"Arm
-#' <k>"} for the selected arm. } A \code{ggplot2::theme_bw()} theme is applied
-#' by default.
-#' @section Dependencies: This method requires both \pkg{GGally} and
-#' \pkg{ggplot2}. If either package is not installed, the method throws an
-#' error with an installation message.
+#' @section Panel layout: The plot matrix is configured as follows: \itemize{
+#' \item upper triangle: scatterplots, \item diagonal: histograms showing
+#' the marginal distribution of each endpoint, \item lower triangle: Pearson
+#' correlation coefficients, \item title: \code{"Arm <k>"} for the selected
+#' arm. }
 #' @seealso \code{\link[=summary.makeDataSim]{summary.makeDataSim}} for
 #' numerical summaries of the simulated data.
 #' @examples
@@ -1517,13 +1513,6 @@ plot.makeDataSim <- function(x,
                              names = NULL,
                              ...) {
 
-  if (!requireNamespace("GGally", quietly = TRUE)) {
-    stop("Package 'GGally' is required for plot.makeDataSim(). Please install it.")
-  }
-  if (!requireNamespace("ggplot2", quietly = TRUE)) {
-    stop("Package 'ggplot2' is required for plot.makeDataSim(). Please install it.")
-  }
-
   dat  <- x$data
   meta <- x$meta
 
@@ -1553,17 +1542,36 @@ plot.makeDataSim <- function(x,
     colnames(dat_sub) <- names
   }
 
-  p <- GGally::ggpairs(
+  panel_cor <- function(x, y, ...) {
+    r   <- round(stats::cor(x, y, use = "pairwise.complete.obs"), 3)
+    usr <- graphics::par("usr")
+    graphics::text(
+      x = (usr[1] + usr[2]) / 2,
+      y = (usr[3] + usr[4]) / 2,
+      labels = paste0("Corr: ", r),
+      cex = 1.2
+    )
+  }
+
+  panel_hist <- function(x, ...) {
+    usr <- graphics::par("usr")
+    on.exit(graphics::par(usr = usr))
+    graphics::par(usr = c(usr[1:2], 0, 1.5))
+    h <- graphics::hist(x, plot = FALSE)
+    breaks <- h$breaks
+    n_breaks <- length(breaks)
+    y <- h$counts / max(h$counts)
+    graphics::rect(breaks[-n_breaks], 0, breaks[-1], y, col = "grey80", border = "white")
+  }
+
+  graphics::pairs(
     dat_sub,
-    upper = list(continuous = "points"),
-    lower = list(continuous = "cor"),
-    progress = FALSE,
+    main = paste0("Arm ", arm_lbl),
+    upper.panel = graphics::points,
+    lower.panel = panel_cor,
+    diag.panel = panel_hist,
     ...
-  ) +
-    ggplot2::theme_bw() +
-    ggplot2::ggtitle(paste0("Arm ", arm_lbl))
-
-  p
+  )
 }