ggplot2: Boxplots with points and fill separation [duplicate]

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")