ggplot2: Boxplots with points and fill separation [duplicate]

Question

I have a data which can be divaded via two seperators. One is year and second is a field characteristics.

box<-as.data.frame(1:36)

box$year <- c(1996,1996,1996,1996,1996,1996,1996,1996,1996,
              1997,1997,1997,1997,1997,1997,1997,1997,1997,
              1996,1996,1996,1996,1996,1996,1996,1996,1996,
              1997,1997,1997,1997,1997,1997,1997,1997,1997)
box$year <- as.character(box$year)

box$case <- c(6.40,6.75,6.11,6.33,5.50,5.40,5.83,4.57,5.80,
              6.00,6.11,6.40,7.00,NA,5.44,6.00,  NA,6.00,
              6.00,6.20,6.40,6.64,6.33,6.60,7.14,6.89,7.10,
              6.73,6.27,6.64,6.41,6.42,6.17,6.05,5.89,5.82)

box$code <- c("L","L","L","L","L","L","L","L","L","L","L","L",
              "L","L","L","L","L","L","M","M","M","M","M","M",
              "M","M","M","M","M","M","M","M","M","M","M","M")

colour <- factor(box$code, labels = c("#F8766D", "#00BFC4"))

In boxplots, I want to display points over them, to see how data is distributed. That is easily done with one single boxplot for every year:

ggplot(box, aes(x = year, y = case, fill = "#F8766D")) +
  geom_boxplot(alpha = 0.80) +
  geom_point(colour = colour, size = 5) +
  theme(text = element_text(size = 18),
        axis.title.x = element_blank(),
        axis.title.y = element_blank(),
        panel.grid.minor.x = element_blank(),
        panel.grid.major.x = element_blank(),
        legend.position = "none")

But it become more complicated as I add fill parameter in them:

ggplot(box, aes(x = year, y = case, fill = code)) +
  geom_boxplot(alpha = 0.80) +
  geom_point(colour = colour, size = 5) +
  theme(text = element_text(size = 18),
        axis.title.x = element_blank(),
        axis.title.y = element_blank(),
        panel.grid.minor.x = element_blank(),
        panel.grid.major.x = element_blank(),
        legend.position = "none")

And now the question: How to move these points to boxplot axes, where they belong? As blue points to blue boxplot and red to red one.

Answer 1

Like Henrik said, use position_jitterdodge() and shape = 21. You can clean up your code a bit too:

1. No need to define box, then fill it piece by piece

2. You can let ggplot hash out the colors if you wish and skip constructing the colors factor. If you want to change the defaults, look into scale_fill_manual and scale_color_manual.

   box <- data.frame(year = c(1996,1996,1996,1996,1996,1996,1996,1996,1996,
                     1997,1997,1997,1997,1997,1997,1997,1997,1997,
                     1996,1996,1996,1996,1996,1996,1996,1996,1996,
                     1997,1997,1997,1997,1997,1997,1997,1997,1997),
                     case  = c(6.40,6.75,6.11,6.33,5.50,5.40,5.83,4.57,5.80,
                     6.00,6.11,6.40,7.00,NA,5.44,6.00,  NA,6.00,
                     6.00,6.20,6.40,6.64,6.33,6.60,7.14,6.89,7.10,
                     6.73,6.27,6.64,6.41,6.42,6.17,6.05,5.89,5.82),
                     code = c("L","L","L","L","L","L","L","L","L","L","L","L",
                     "L","L","L","L","L","L","M","M","M","M","M","M",
                     "M","M","M","M","M","M","M","M","M","M","M","M"))
   
   ggplot(box, aes(x = factor(year), y = case, fill = code)) +
     geom_boxplot(alpha = 0.80) +
     geom_point(aes(fill = code), size = 5, shape = 21, position = position_jitterdodge()) +
     theme(text = element_text(size = 18),
           axis.title.x = element_blank(),
           axis.title.y = element_blank(),
           panel.grid.minor.x = element_blank(),
           panel.grid.major.x = element_blank(),
           legend.position = "none")
   

Answer 2

I see you've already accepted @JakeKaupp's nice answer, but I thought I would throw in a different option, using geom_dotplot. The data you are visualizing is rather small, so why not forego the boxplot?

ggplot(box, aes(x = factor(year), y = case, fill = code))+
    geom_dotplot(binaxis = 'y', stackdir = 'center',
                 position = position_dodge())