Data Visualization using GGPlot2

GGPlot Violin Plot

A Violin Plot is used to visualize the distribution of the data and its probability density.

This chart is a combination of a Box plot and a Density Plot that is rotated and placed on each side, to display the distribution shape of the data.

Typically, violin plots will include a marker for the median of the data and a box indicating the interquartile range, as in standard boxplots.

A Violin Plot shows more information than a Box Plot. For example, in a violin plot, you can see whether the distribution of the data is bimodal or multimodal.

This article describes how to create and customize violin plots using the ggplot2 R package.

Contents:

Related Book

GGPlot2 Essentials for Great Data Visualization in R

Key R functions

Key function:

  • geom_violin(): Creates violin plots. Key arguments:
    • color, size, linetype: Border line color, size and type
    • fill: Areas fill color
    • trim: logical value. If TRUE (default), trim the tails of the violins to the range of the data. If FALSE, don’t trim the tails.
  • stat_summary(): Adds summary statistics (mean, median, …) on the violin plots.

Data preparation

  • Demo dataset: ToothGrowth
    • Continuous variable: len (tooth length). Used on y-axis
    • Grouping variable: dose (dose levels of vitamin C: 0.5, 1, and 2 mg/day). Used on x-axis.

First, convert the variable dose from a numeric to a discrete factor variable:

data("ToothGrowth")
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
head(ToothGrowth, 4)
##    len supp dose
## 1  4.2   VC  0.5
## 2 11.5   VC  0.5
## 3  7.3   VC  0.5
## 4  5.8   VC  0.5

Loading required R package

Load the ggplot2 package and set the default theme to theme_classic() with the legend at the top of the plot:

library(ggplot2)
theme_set(
  theme_classic() +
    theme(legend.position = "top")
  )

Basic violin plots

We start by initiating a plot named e, then we’ll add layers. The following R code creates Violin Plots combined with summary statistics (mean +/- SD) and Box Plots.

Create basic violin plots with summary statistics:

# Initiate a ggplot
e <- ggplot(ToothGrowth, aes(x = dose, y = len))

# Add mean points +/- SD
# Use geom = "pointrange" or geom = "crossbar"
e + geom_violin(trim = FALSE) + 
  stat_summary(
    fun.data = "mean_sdl",  fun.args = list(mult = 1), 
    geom = "pointrange", color = "black"
    )
    
# Combine with box plot to add median and quartiles
# Change fill color by groups, remove legend
e + geom_violin(aes(fill = dose), trim = FALSE) + 
  geom_boxplot(width = 0.2)+
  scale_fill_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))+
  theme(legend.position = "none")

The function mean_sdl is used for adding mean and standard deviation. It computes the mean plus or minus a constant times the standard deviation. In the R code above, the constant is specified using the argument mult (mult = 1). By default mult = 2. The mean +/- SD can be added as a crossbar or a pointrange.

Create a Violin Plot with multiple groups

Two different grouping variables are used: dose on x-axis and supp as line color (legend variable).

The space between the grouped plots is adjusted using the function position_dodge().

e + geom_violin(aes(color = supp), trim = FALSE, position = position_dodge(0.9) ) +
  geom_boxplot(aes(color = supp), width = 0.15, position = position_dodge(0.9)) +
  scale_color_manual(values = c("#00AFBB", "#E7B800"))

Conclusion

This article describes how to create a Violin Plot using the ggplot2 package.

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Alboukadel Kassambara
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