How to generate a jitterplot similar to this one in R?

Question

I want to reproduce a jitterplot in R similar to the one described in Figure 1a of Zack et al., Nature Genetics, 2013:

I tried the beeswarm functino and the pirate function. The beeswarm function lines the points up to straight and they look like a line has been drawn. I also tried the Pirateplot function and I generally like it, however, I did not figure out how to change the color of different points based on their value on the y-axis as done in the plot from the reference paper.

Eventually, the points should be scattered like in the pirate plot, but colorcoded according to their value on the y-axis.

Anyone any suggestions?

Thanks Tom

Answer 1

I think ggplot2 is the best package to create a jitter plot.

ids <- c(
  rep("id1", 20), 
  rep("id2", 20), 
  rep("id3", 20)
)

values <- runif(60)

classes <- c(
  rep("class1", 30), 
  rep("class2", 30)
)

data <- data.frame(ids, values, classes)

library(ggplot2)

ggplot(data) +
  geom_jitter(
    aes(ids, values, color = classes), 
    width = 0.1
  )