Restrain scattered jitter points within a violin plot by ggplot2

Question

A following is used to generate the violin plot in ggplot2 :

ggplot(violin,aes(x=variable,y=log(value+0.5),color=Group)) + 
  geom_violin(scale="width") + 
  geom_jitter(aes(group=Group), position=position_jitterdodge()) + 
  stat_summary(fun.y="mean",geom="crossbar", mapping=aes(ymin=..y.., ymax=..y..), 
     width=1, position=position_dodge(),show.legend = FALSE) + 
  theme(axis.text.x = element_text(angle = 45, margin=margin(0.5, unit="cm")))

A resulting plot looks like following;

As you can see, some points are jittered outside the boundary of violin shape and I need to those points to be inside of the violin. I've played different levels of jittering but have had any success. I'd appreciate any pointers to achieve this.

Answer 1

The package ggbeeswarm has the geoms quasirandom and beeswarm, which do exactly what you are searching for: https://github.com/eclarke/ggbeeswarm

Answer 2

It is a little bit old question but I think there is a better solution.

As @Richard Telford pointed out in a comment, geom_sina is the best solution IMO.

simulate data

df <- data.frame(data=rnorm(1200), 
                 group=rep(c("A","A","A", "B","B","C"),
                           200)
                 )

make plot

ggplot(df, aes(y=data,x=group,color=group)) +
  geom_violin()+
  geom_sina()

result

Hope this is helpful.

Answer 3

Option 1

Using the function geom_quasirandom from package geom_beeswarm:

The quasirandom geom is a convenient means to offset points within categories to reduce overplotting. Uses the vipor package.

library(ggbeeswarm)
p <- ggplot(mpg, aes(class, hwy))
p + geom_violin(width = 1.3) + geom_quasirandom(alpha = 0.2, width = 0.2)

Option 2

Not a satisfactory answer, because by restricting the horizontal jitter we defeat the purpose of handling overplotting. But you can enlarge the width of the violin plots (width = 1.3), and play with alpha for transparency and limit the horizontal jitter (width = .02).

p <- ggplot(mpg, aes(class, hwy))
p + geom_violin(width = 1.3) + geom_jitter(alpha = 0.2, width = .02)