Building off of my previous question, with thanks to @AndrewGB for the code modifications (

CodePudding user response：

You can use the breaks argument of scale_fill_manual to limit the number of legend entries without limiting the actual plotted colors. However, you need to name the colors in the values argument explicitly:

library(tidyverse)
library(data.table)
#> 
#> Attaching package: 'data.table'
#> The following objects are masked from 'package:dplyr':
#> 
#>     between, first, last
#> The following object is masked from 'package:purrr':
#> 
#>     transpose

dat <- as.data.table(cbind(iris, Status = rep(c("High", "Low"), 75)))
dat <- rbind(dat, data.frame(
  Petal.Width = sample(iris$Petal.Width, 30, replace = T),
  Species = "Control",
  Status = "Control"
), fill = T)

dat %>%
  mutate(fill = Species %>% paste0(Status)) %>%
  ggplot(aes(x = Species, y = Petal.Width, fill = fill))  
  geom_boxplot()  
  scale_fill_manual(
    values = c(
      setosaHigh = "red", setosaLow = "pink",
      versicolorHigh = "lightgreen", versicolorLow = "darkgreen",
      virginicaHigh = "darkblue", virginicaLow = "lightblue",
      ControlControl = "purple"
    ),
    breaks = c("virginicaLow", "virginicaHigh", "ControlControl")
  )

^{Created on 2022-05-10 by the reprex package (v2.0.0)}