From 340d08789aec20fe8bf0bbe5508f384656a96208 Mon Sep 17 00:00:00 2001
From: hanneoberman <h.i.oberman@uu.nl>
Date: Mon, 22 Jan 2024 11:24:41 +0100
Subject: [PATCH 1/2] set `fill` aesthetic to `mice` colors

---
 R/ggmice.R    | 19 ++++++++++++++++---
 man/ggmice.Rd |  4 +++-
 2 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/R/ggmice.R b/R/ggmice.R
index 3ab1862e..1fd37d73 100644
--- a/R/ggmice.R
+++ b/R/ggmice.R
@@ -7,9 +7,11 @@
 #' equivalent to [`ggplot2::ggplot`] output, with a few important exceptions:
 #'
 #' - The theme is set to [`ggmice::theme_mice`].
-#' - The color scale is set to the [`mice::mdc`] colors.
+#' - The color and fill scales are set to the [`mice::mdc`] colors (see below).
 #' - The `colour` aesthetic is set to `.where`, an internally defined variable which distinguishes
 #' observed data from missing data or imputed data (for incomplete and imputed data, respectively).
+#' - The `fill` aesthetic is set to `.where`, an internally defined variable which distinguishes
+#' observed data from missing data or imputed data (for incomplete and imputed data, respectively).
 #'
 #' @examples
 #' dat <- mice::nhanes
@@ -48,6 +50,14 @@ ggmice <- function(data = NULL,
       )
     )
   }
+  if (!is.null(mapping$fill)) {
+    cli::cli_warn(
+      c(
+        "The aes() argument 'fill' has a special use in ggmice() and will be overwritten.",
+        "i" = "Try using 'shape' or 'linetype' for additional mapping, or use faceting."
+      )
+    )
+  }
 
   # extract variable names from mapping object
   if (is.data.frame(data)) {
@@ -91,7 +101,7 @@ ggmice <- function(data = NULL,
       )
     }
     mice_mapping <-
-      utils::modifyList(mapping, ggplot2::aes(colour = .where))
+      utils::modifyList(mapping, ggplot2::aes(colour = .where, fill = .where))
     mice_colors <-
       c("observed" = "#006CC2B3",
         "missing" = "#B61A51B3")
@@ -118,7 +128,7 @@ ggmice <- function(data = NULL,
       .imp = factor(.imp, levels = 0:data$m, ordered = TRUE)
     )
     mice_mapping <-
-      utils::modifyList(mapping, ggplot2::aes(colour = .where))
+      utils::modifyList(mapping, ggplot2::aes(colour = .where, fill = .where))
     mice_colors <-
       c("observed" = "#006CC2B3",
         "imputed" = "#B61A51B3")
@@ -129,6 +139,9 @@ ggmice <- function(data = NULL,
     ggplot2::scale_color_manual(values = mice_colors,
                                 name = "",
                                 drop = FALSE) +
+    ggplot2::scale_fill_manual(values = mice_colors,
+                               name = "",
+                               drop = FALSE) +
     theme_mice()
 
   # edit plot to display missing values on the axes
diff --git a/man/ggmice.Rd b/man/ggmice.Rd
index 523e8005..53d00523 100644
--- a/man/ggmice.Rd
+++ b/man/ggmice.Rd
@@ -16,9 +16,11 @@ An object of class \code{\link[ggplot2:ggplot]{ggplot2::ggplot}}. The \code{\lin
 equivalent to \code{\link[ggplot2:ggplot]{ggplot2::ggplot}} output, with a few important exceptions:
 \itemize{
 \item The theme is set to \code{\link{theme_mice}}.
-\item The color scale is set to the \code{\link[mice:mdc]{mice::mdc}} colors.
+\item The color and fill scales are set to the \code{\link[mice:mdc]{mice::mdc}} colors (see below).
 \item The \code{colour} aesthetic is set to \code{.where}, an internally defined variable which distinguishes
 observed data from missing data or imputed data (for incomplete and imputed data, respectively).
+\item The \code{fill} aesthetic is set to \code{.where}, an internally defined variable which distinguishes
+observed data from missing data or imputed data (for incomplete and imputed data, respectively).
 }
 }
 \description{

From 9e79593969ee10b2e4849f2fd664804d491348aa Mon Sep 17 00:00:00 2001
From: hanneoberman <h.i.oberman@uu.nl>
Date: Mon, 22 Jan 2024 14:06:50 +0100
Subject: [PATCH 2/2] add `mice` color to `na.value`

---
 R/ggmice.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/ggmice.R b/R/ggmice.R
index 1fd37d73..ddddd986 100644
--- a/R/ggmice.R
+++ b/R/ggmice.R
@@ -137,9 +137,11 @@ ggmice <- function(data = NULL,
   # create plot
   gg <- ggplot2::ggplot(data = mice_data, mapping = mice_mapping) +
     ggplot2::scale_color_manual(values = mice_colors,
+                                na.value = "#B61A51B3",
                                 name = "",
                                 drop = FALSE) +
     ggplot2::scale_fill_manual(values = mice_colors,
+                               na.value = "#B61A51B3",
                                name = "",
                                drop = FALSE) +
     theme_mice()