ggplot2: How to get dots to group with violin plots?

8
votes

I would like to plot violin plots where x axis is exon however I want to group the plots. This works if its just violins however when I add in the jitters for some reason its not responding the correct aes and is plotting on its own? Here is a reproducible code with a screen shot of the error. thanks! 

set.seed(1)
df <- data.frame(
  exons = c(rep("e1", 200), rep("e2", 200)),
  values = rnorm(400, 200, 40),
  group = c(
    rep("g1", 75), rep("g2", 75), rep("g3", 50),
    rep("g1", 75), rep("g2", 75), rep("g3", 50)
  )
)

ggplot(df, aes(y = values, x = exons, fill = group)) +
  geom_violin() +
  geom_jitter(shape = 16, position = position_jitter(0.07))

so if the plot works the dots should had been plotted within each of the group for each exon, however here it is clearly not.

enter image description here

2
rggplot2violin-plot

2 Answers

4
votes

You probably want both position_dodge() and position_jitterdodge()

library(ggplot2)
ggplot(df, aes(y = values, x = exons, fill = group)) +
  geom_violin(position = position_dodge(width = 0.9)) +
  geom_point(position = position_jitterdodge(seed = 1, dodge.width = 0.9))

Another option worth mentioning is geom_quasirandom() function from the ggbeeswarm package

library(ggbeeswarm)
ggplot(df, aes(y = values, x = exons, fill = group)) +
  geom_violin(position = position_dodge(width = 0.9)) +
  geom_quasirandom(dodge.width = 0.9, varwidth = TRUE)

Created on 2019-08-10 by the reprex package (v0.3.0)

0
votes

Do you mean something like that? 

set.seed ( 1)
df = data.frame ( 
  exons = c(rep("e1", 200), rep("e2", 200))
  ,values = rnorm(400,200,40)
  ,group = c(rep("g1", 75), rep("g2", 75), rep("g3",50),
             rep("g1", 75), rep("g2", 75), rep("g3",50) )
)

ggplot(df, aes(y= values  , x= exons , fill = group )) +
  geom_violin()+ 
  geom_jitter(shape=16, position=position_jitter(width = NULL, height = NULL))

You can define the degree of jitter in x and y direction.