From e2ae8ac2320d20efc4f414d846c7c5455e5bb460 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <tahvdbrand@gmail.com>
Date: Thu, 18 Apr 2024 14:33:30 +0200
Subject: [PATCH 1/5] protect against early NAs

---
 R/scale-.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/R/scale-.R b/R/scale-.R
index 0b374d72ef..08ee0efa53 100644
--- a/R/scale-.R
+++ b/R/scale-.R
@@ -961,6 +961,12 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale,
         )
       }
       pal <- self$palette(n)
+      if (n != length(limits)) {
+        # ensure NAs in non-end positions are reinserted
+        tmp <- rep(vec_cast(self$na.value, pal), length(limits))
+        tmp[!is.na(limits)] <- pal
+        pal <- tmp
+      }
       self$palette.cache <- pal
       self$n.breaks.cache <- n
     }

From 92decaec18c220c31731d3898db6dd712eac7078 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <tahvdbrand@gmail.com>
Date: Thu, 18 Apr 2024 14:57:04 +0200
Subject: [PATCH 2/5] add test

---
 tests/testthat/test-scales.R | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R
index 691f0920aa..782a4bc3bb 100644
--- a/tests/testthat/test-scales.R
+++ b/tests/testthat/test-scales.R
@@ -730,3 +730,28 @@ test_that("Discrete scales with only NAs return `na.value`", {
   sc$train(x)
   expect_equal(sc$map(x), c(NA_real_, NA_real_))
 })
+
+test_that("discrete scales work with NAs in arbitrary positions", {
+  # Prevents intermediate caching of palettes
+  map <- function(x, limits) {
+    sc <- scale_colour_manual(
+      values = c("red", "green", "blue"),
+      na.value = "gray"
+    )
+    sc$map(x, limits)
+  }
+
+  # All inputs should yield output regardless of where NA is
+  input  <- c("A", "B", "C", NA)
+  output <- c("red", "green", "blue", "gray")
+
+  test <- map(x, limits = c("A", "B", "C", NA))
+  expect_equal(test, output)
+
+  test <- map(x, limits = c("A", NA, "B", "C"))
+  expect_equal(test, output)
+
+  test <- map(x, limits = c(NA, "A", "B", "C"))
+  expect_equal(test, output)
+
+})

From 8cc991c2317ce4df944e53199b0aa6510c568330 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <tahvdbrand@gmail.com>
Date: Thu, 18 Apr 2024 15:12:06 +0200
Subject: [PATCH 3/5] add news bullet

---
 NEWS.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index eef76f1cec..10ac0cabb9 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,8 @@
 
 # ggplot2 (development version)
 
+* Fixed bug where `na.value` was incorrectly mapped to non-`NA` values 
+  (@teunbrand, #5756).
 * When facets coerce the faceting variables to factors, the 'ordered' class
   is dropped (@teunbrand, #5666).
 * `coord_map()` and `coord_polar()` throw informative warnings when used

From 85e3506bd5aaaceee238ee8131c20325ec049e83 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <tahvdbrand@gmail.com>
Date: Thu, 18 Apr 2024 15:19:13 +0200
Subject: [PATCH 4/5] fix typos

---
 tests/testthat/test-scales.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R
index 782a4bc3bb..79bd27af22 100644
--- a/tests/testthat/test-scales.R
+++ b/tests/testthat/test-scales.R
@@ -745,13 +745,13 @@ test_that("discrete scales work with NAs in arbitrary positions", {
   input  <- c("A", "B", "C", NA)
   output <- c("red", "green", "blue", "gray")
 
-  test <- map(x, limits = c("A", "B", "C", NA))
+  test <- map(input, limits = c("A", "B", "C", NA))
   expect_equal(test, output)
 
-  test <- map(x, limits = c("A", NA, "B", "C"))
+  test <- map(input, limits = c("A", NA, "B", "C"))
   expect_equal(test, output)
 
-  test <- map(x, limits = c(NA, "A", "B", "C"))
+  test <- map(input, limits = c(NA, "A", "B", "C"))
   expect_equal(test, output)
 
 })

From baa2a98f8a6095ee303502577aa33af97f7a8a3c Mon Sep 17 00:00:00 2001
From: Teun van den Brand <tahvdbrand@gmail.com>
Date: Thu, 18 Apr 2024 15:20:59 +0200
Subject: [PATCH 5/5] simplify by discarding `NA` limits

---
 R/scale-.R | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/R/scale-.R b/R/scale-.R
index 08ee0efa53..6233caf54f 100644
--- a/R/scale-.R
+++ b/R/scale-.R
@@ -947,7 +947,8 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale,
   transform = identity,
 
   map = function(self, x, limits = self$get_limits()) {
-    n <- sum(!is.na(limits))
+    limits <- limits[!is.na(limits)]
+    n <- length(limits)
     if (n < 1) {
       return(rep(self$na.value, length(x)))
     }
@@ -961,12 +962,6 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale,
         )
       }
       pal <- self$palette(n)
-      if (n != length(limits)) {
-        # ensure NAs in non-end positions are reinserted
-        tmp <- rep(vec_cast(self$na.value, pal), length(limits))
-        tmp[!is.na(limits)] <- pal
-        pal <- tmp
-      }
       self$palette.cache <- pal
       self$n.breaks.cache <- n
     }