From 3b8e1a14d697842cc354dd5014134406807cb9f4 Mon Sep 17 00:00:00 2001
From: Paul Schmidt <schmidtpaul@hotmail.de>
Date: Wed, 5 Aug 2026 11:45:44 +0200
Subject: [PATCH] ggdesplot: leave cells with a missing value empty

The gg path filled a missing value with grey50, which is hard to tell from the
lightgray midpoint of the default RedGrayBlue scale, so a hole in the field
read as a mid-range value. The lattice path leaves such a cell empty; set
na.value on both fill scales to match it.
---
 NEWS.md                               |  2 ++
 R/ggdesplot.R                         |  8 ++++++--
 tests/testthat/test_ggdesplot_fixes.R | 20 ++++++++++++++++++++
 3 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index e3c6b96..c24bf83 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
 # desplot 1.11 ()
 
+* `ggdesplot()` now leaves cells with a missing value empty, as `desplot()` does. Previously they were filled with the ggplot2 default grey, which lies inside the range of the default red-gray-blue scale and so looked like a mid-range value. (P.Schmidt)
+
 * `ggdesplot()` no longer draws a spurious `no_color` legend when `text` or `num` is used without `col`. (P.Schmidt)
 
 * `ggdesplot()` now facets on every conditioning variable in a formula such as `yield ~ col*row | site + rep`. Previously only the first was used and the others were silently dropped, overplotting cells. (P.Schmidt)
diff --git a/R/ggdesplot.R b/R/ggdesplot.R
index 57ad951..25bf8d1 100644
--- a/R/ggdesplot.R
+++ b/R/ggdesplot.R
@@ -482,17 +482,21 @@ ggdesplot <- function(data,
     out <- out + 
       facet_wrap(panel.string, scales="free")
   
+  # Note, cells with a missing value are left empty instead of being filled
+  # with the ggplot2 default grey50, which is hard to tell from the lightgray
+  # midpoint of RedGrayBlue. The lattice version leaves such cells empty too.
   if(fill.type=="num")
     out <- out +
     #geom_tile(aes_string(fill = fill.string)) +
     geom_tile(aes(fill = .data[[fill.string]])) +
-    scale_fill_gradientn(colours=col.regions, guide="colorbar")
+    scale_fill_gradientn(colours=col.regions, guide="colorbar",
+                         na.value="transparent")
   
   if(fill.type=="factor")
     out <- out +
     #geom_tile(aes_string(fill = fill.string)) +
     geom_tile(aes(fill = .data[[fill.string]])) +
-    scale_fill_manual(values=col.regions)
+    scale_fill_manual(values=col.regions, na.value="transparent")
   
   if(has.out1)
     out <- out +
diff --git a/tests/testthat/test_ggdesplot_fixes.R b/tests/testthat/test_ggdesplot_fixes.R
index 5584aa1..7a9df80 100644
--- a/tests/testthat/test_ggdesplot_fixes.R
+++ b/tests/testthat/test_ggdesplot_fixes.R
@@ -44,3 +44,23 @@ test_that("ggdesplot single conditioning variable keeps its panel labels", {
   p <- suppressWarnings(ggdesplot(besag.met, yield ~ col * row | county))
   expect_equal(levels(p$data$.panel), paste0("C", 1:6))
 })
+
+test_that("ggdesplot leaves a cell with a missing value empty", {
+  # 4x4 field with a hole at col 2 / row 2, once numeric and once a factor
+  hole <- data.frame(
+    col = rep(1:4, times = 4),
+    row = rep(1:4, each = 4),
+    yield = c(1:5, NA, 7:16),
+    B = factor(c(rep("b1", 5), NA, rep("b2", 10)))
+  )
+
+  fill_num <- ggplot2::layer_data(ggdesplot(hole, yield ~ col * row), 1)$fill
+  expect_equal(sum(fill_num == "transparent"), 1L)
+  # the guard: the other 15 cells still get a real colour from col.regions,
+  # so the empty cell comes from the missing value and not from a broken scale
+  expect_equal(length(unique(fill_num[fill_num != "transparent"])), 15L)
+
+  fill_fac <- ggplot2::layer_data(ggdesplot(hole, B ~ col * row), 1)$fill
+  expect_equal(sum(fill_fac == "transparent"), 1L)
+  expect_equal(length(unique(fill_fac[fill_fac != "transparent"])), 2L)
+})