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.

where does the data `violin` come from? – dww Jun 27 '18 at 19:30 — dww, Jun 27 '18 at 19:30
maybe try `ggforce::geom_sina` – Richard Telford Jun 27 '18 at 19:31 — Richard Telford, Jun 27 '18 at 19:31

score 9 · Answer 1 · answered Jun 27 '18 at 19:41

9

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

answered Jun 27 '18 at 19:41

Jannik Buhr

1,788
2
11
11

score 6 · Accepted Answer · answered Mar 13 '20 at 15:51

6

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.

answered Mar 13 '20 at 15:51

Alfonso

644
7
17

1

Hi @akh22, I am glad it works for you. If you like the answer you may want to upvote and/or mark as the answer to your question. Thanks – Alfonso May 14 '20 at 15:58

mpalanco · Answer 3 · 2019-01-31T08:07:46.313

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)

Restrain scattered jitter points within a violin plot by ggplot2

3 Answers3