diff --git a/NEWS.md b/NEWS.md
index 1639c55642..30b5175682 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,9 @@
 # ggplot2 (development version)
 
+* Manual scales now allow named vectors passed to `values` to contain fewer 
+  elements than existing in the data. Elements not present in values will be set
+  to `NA` (@thomasp85, #3451)
+  
 * Remove cross-inheritance of default discrete colour/fill scales and check the
   type and aesthetic of function output if `type` is a function 
   (@thomasp85, #4149)
diff --git a/R/scale-manual.r b/R/scale-manual.r
index ffd3fcda2a..63e2839371 100644
--- a/R/scale-manual.r
+++ b/R/scale-manual.r
@@ -28,6 +28,8 @@
 #'   - A character vector of breaks
 #'   - A function that takes the limits as input and returns breaks
 #'     as output
+#' @param na.value The aesthetic value to use for missing (`NA`) values
+#'
 #' @section Color Blindness:
 #' Many color palettes derived from RGB combinations (like the "rainbow" color
 #' palette) are not suitable to support all viewers, especially those with
@@ -80,38 +82,38 @@ NULL
 
 #' @rdname scale_manual
 #' @export
-scale_colour_manual <- function(..., values, aesthetics = "colour", breaks = waiver()) {
-  manual_scale(aesthetics, values, breaks, ...)
+scale_colour_manual <- function(..., values, aesthetics = "colour", breaks = waiver(), na.value = "grey50") {
+  manual_scale(aesthetics, values, breaks, ..., na.value = na.value)
 }
 
 #' @rdname scale_manual
 #' @export
-scale_fill_manual <- function(..., values, aesthetics = "fill", breaks = waiver()) {
-  manual_scale(aesthetics, values, breaks, ...)
+scale_fill_manual <- function(..., values, aesthetics = "fill", breaks = waiver(), na.value = "grey50") {
+  manual_scale(aesthetics, values, breaks, ..., na.value = na.value)
 }
 
 #' @rdname scale_manual
 #' @export
-scale_size_manual <- function(..., values, breaks = waiver()) {
-  manual_scale("size", values, breaks, ...)
+scale_size_manual <- function(..., values, breaks = waiver(), na.value = NA) {
+  manual_scale("size", values, breaks, ..., na.value = na.value)
 }
 
 #' @rdname scale_manual
 #' @export
-scale_shape_manual <- function(..., values, breaks = waiver()) {
-  manual_scale("shape", values, breaks, ...)
+scale_shape_manual <- function(..., values, breaks = waiver(), na.value = NA) {
+  manual_scale("shape", values, breaks, ..., na.value = na.value)
 }
 
 #' @rdname scale_manual
 #' @export
-scale_linetype_manual <- function(..., values, breaks = waiver()) {
-  manual_scale("linetype", values, breaks, ...)
+scale_linetype_manual <- function(..., values, breaks = waiver(), na.value = "blank") {
+  manual_scale("linetype", values, breaks, ..., na.value = na.value)
 }
 
 #' @rdname scale_manual
 #' @export
-scale_alpha_manual <- function(..., values, breaks = waiver()) {
-  manual_scale("alpha", values, breaks, ...)
+scale_alpha_manual <- function(..., values, breaks = waiver(), na.value = NA) {
+  manual_scale("alpha", values, breaks, ..., na.value = na.value)
 }
 
 #' @rdname scale_manual
@@ -121,7 +123,7 @@ scale_discrete_manual <- function(aesthetics, ..., values, breaks = waiver()) {
 }
 
 
-manual_scale <- function(aesthetic, values = NULL, breaks = waiver(), ...) {
+manual_scale <- function(aesthetic, values = NULL, breaks = waiver(), limits = NULL, ...) {
   # check for missing `values` parameter, in lieu of providing
   # a default to all the different scale_*_manual() functions
   if (is_missing(values)) {
@@ -130,6 +132,10 @@ manual_scale <- function(aesthetic, values = NULL, breaks = waiver(), ...) {
     force(values)
   }
 
+  if (is.null(limits)) {
+    limits <- names(values)
+  }
+
   # order values according to breaks
   if (is.vector(values) && is.null(names(values)) && !is.waive(breaks) &&
       !is.null(breaks) && !is.function(breaks)) {
@@ -146,5 +152,5 @@ manual_scale <- function(aesthetic, values = NULL, breaks = waiver(), ...) {
     }
     values
   }
-  discrete_scale(aesthetic, "manual", pal, breaks = breaks, ...)
+  discrete_scale(aesthetic, "manual", pal, breaks = breaks, limits = limits, ...)
 }
diff --git a/man/scale_manual.Rd b/man/scale_manual.Rd
index ad9a742df3..b4386bbc58 100644
--- a/man/scale_manual.Rd
+++ b/man/scale_manual.Rd
@@ -11,17 +11,29 @@
 \alias{scale_color_manual}
 \title{Create your own discrete scale}
 \usage{
-scale_colour_manual(..., values, aesthetics = "colour", breaks = waiver())
+scale_colour_manual(
+  ...,
+  values,
+  aesthetics = "colour",
+  breaks = waiver(),
+  na.value = "grey50"
+)
 
-scale_fill_manual(..., values, aesthetics = "fill", breaks = waiver())
+scale_fill_manual(
+  ...,
+  values,
+  aesthetics = "fill",
+  breaks = waiver(),
+  na.value = "grey50"
+)
 
-scale_size_manual(..., values, breaks = waiver())
+scale_size_manual(..., values, breaks = waiver(), na.value = NA)
 
-scale_shape_manual(..., values, breaks = waiver())
+scale_shape_manual(..., values, breaks = waiver(), na.value = NA)
 
-scale_linetype_manual(..., values, breaks = waiver())
+scale_linetype_manual(..., values, breaks = waiver(), na.value = "blank")
 
-scale_alpha_manual(..., values, breaks = waiver())
+scale_alpha_manual(..., values, breaks = waiver(), na.value = NA)
 
 scale_discrete_manual(aesthetics, ..., values, breaks = waiver())
 }
@@ -47,9 +59,6 @@ The default, \code{TRUE}, uses the levels that appear in the data;
     \item{\code{na.translate}}{Unlike continuous scales, discrete scales can easily show
 missing values, and do so by default. If you want to remove missing values
 from a discrete scale, specify \code{na.translate = FALSE}.}
-    \item{\code{na.value}}{If \code{na.translate = TRUE}, what aesthetic value should the
-missing values be displayed as? Does not apply to position scales
-where \code{NA} is always placed at the far right.}
     \item{\code{scale_name}}{The name of the scale that should be used for error messages
 associated with this scale.}
     \item{\code{name}}{The name of the scale. Used as the axis or legend title. If
@@ -90,6 +99,8 @@ same time, via \code{aesthetics = c("colour", "fill")}.}
 \item A function that takes the limits as input and returns breaks
 as output
 }}
+
+\item{na.value}{The aesthetic value to use for missing (\code{NA}) values}
 }
 \description{
 These functions allow you to specify your own set of mappings from levels in the
diff --git a/tests/testthat/test-scale-manual.r b/tests/testthat/test-scale-manual.r
index fecce1de20..b8af871e99 100644
--- a/tests/testthat/test-scale-manual.r
+++ b/tests/testthat/test-scale-manual.r
@@ -88,12 +88,12 @@ test_that("unnamed values match breaks in manual scales", {
 
 test_that("limits works (#3262)", {
   # named charachter vector
-  s1 <- scale_colour_manual(values = c("8" = "c", "4" = "a", "6" = "b"), limits = c("4", "8"))
+  s1 <- scale_colour_manual(values = c("8" = "c", "4" = "a", "6" = "b"), limits = c("4", "8"), na.value = NA)
   s1$train(c("4", "6", "8"))
   expect_equal(s1$map(c("4", "6", "8")), c("a", NA, "c"))
 
   # named charachter vector
-  s2 <- scale_colour_manual(values = c("c", "a", "b"), limits = c("4", "8"))
+  s2 <- scale_colour_manual(values = c("c", "a", "b"), limits = c("4", "8"), na.value = NA)
   s2$train(c("4", "6", "8"))
   expect_equal(s2$map(c("4", "6", "8")), c("c", NA, "a"))
 })