How to fit boxplot inside violon plot in r?

Question

Recently I am doing violin plot combine with box plot in R,

my data is

data = structure(list(Sample.ID = c("S-1", "S-2", "S-3", "S-4", "S-5", 
"S-6", "S-7", "S-8", "S-9", "S-10", "S-11", "S-12", "S-13", "S-1", 
"S-2", "S-3", "S-4", "S-5", "S-6", "S-7", "S-8", "S-9", "S-10", 
"S-11", "S-12", "S-13"), Season = structure(c(2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L), .Label = c("Summer", "Winter"), class = "factor"), 
    D.N = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 
    1L), .Label = c("Day", "Night"), class = "factor"), Tide.type = structure(c(3L, 
    1L, 2L, 2L, 1L, 3L, 3L, 3L, 1L, 2L, 2L, 1L, 3L, 1L, 2L, 2L, 
    2L, 3L, 3L, 3L, 1L, 2L, 2L, 1L, 3L, 3L), .Label = c("Flat", 
    "High", "Low"), class = "factor"), MPs..items.m3. = c(134, 
    144, 154, 156, 142, 122, 114, 148, 146, 152, 112, 108, 104, 
    224, 212, 100, 141.3333333, 193.3333333, 157.3333333, 129.3333333, 
    146.6666667, 188, 93.33333333, 210.6666667, 122.6666667, 
    114.6666667)), row.names = c(NA, -26L), class = "data.frame")

now when I am using the box plot code combine with violin the box is not align inside the violin plot. how to fix it.

My code is

data$Season = as.factor(data$Season)
data$D.N = as.factor(data$D.N)
data$Tide.type = as.factor(data$Tide.type)
str(data)

library(ggplot2)

ggplot(data, aes(x=Season, y=MPs..items.m3.)) +
  geom_violin(aes(fill = D.N),)+
  geom_boxplot(aes(fill = D.N), width = 0.2)

My picture look like this

Answer 1

You need to set the correct width of position_dodge:

ggplot(data, aes(x = Season, y = MPs..items.m3., fill = D.N)) +
  geom_violin(position = position_dodge(0.9)) +
  geom_boxplot(width = 0.1, position = position_dodge(0.9), alpha = 0.5,
               fill = 'white', aes(group = interaction(Season, D.N))) +
  theme_classic(base_size = 16) +
  scale_fill_manual(values = c('orange', 'deepskyblue4'))

Answer 2

If you want your original colors:

ggplot(data, aes(x=Season, y=MPs..items.m3.,fill = D.N)) +
    geom_violin(aes(fill = D.N),position = position_dodge(.9))+
    geom_boxplot(aes(fill = D.N),position = position_dodge(.9),width = 0.2)

Note that if you didn't have two groups / season, you could also just use position = "identity", here this would put all 4 on top of each other / season, so not ideal for your graphic I guess, but here it is just to illustrate the point in case it ever comes up in the future