Prevent mismapping when limits contain NA in non-last position

NEWS.md

@@ -1,5 +1,7 @@
 # ggplot2 (development version)
 
+* Fixed bug where `na.value` was incorrectly mapped to non-`NA` values 
+  (@teunbrand, #5756).
 * Fixed bug in `guide_custom()` that would throw error with `theme_void()` 
   (@teunbrand, #5856).
 * New helper function `ggpar()` to translate ggplot2's interpretation of 

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)))
     }

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(input, limits = c("A", "B", "C", NA))
+  expect_equal(test, output)
+
+  test <- map(input, limits = c("A", NA, "B", "C"))
+  expect_equal(test, output)
+
+  test <- map(input, limits = c(NA, "A", "B", "C"))
+  expect_equal(test, output)
+
+})