Data Visualization using GGPlot2

Key R functions

• Key function: geom_dotplot(). Creates stacked dots, with each dot representing one observation.
• Key arguments:
  • stackdir: which direction to stack the dots. “up” (default), “down”, “center”, “centerwhole” (centered, but with dots aligned).
  • stackratio: how close to stack the dots. Default is 1, where dots just just touch. Use smaller values for closer, overlapping dots.
  • color, fill: Dot border color and area fill
  • dotsize: The diameter of the dots relative to binwidth, default 1.

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 Dot Plots

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

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

# Dotplot with summary statistics: mean +/- SD
e + geom_dotplot(binaxis = "y", stackdir = "center", fill = "lightgray") + 
  stat_summary(fun.data = "mean_sdl", fun.args = list(mult=1))

# dot plots combined with box plots
e + geom_boxplot(width = 0.5) + 
  geom_dotplot(binaxis = "y", stackdir = "center", fill = "lightgray") 

# Dot plot + violin plot + stat summary
e + geom_violin(trim = FALSE) +
  geom_dotplot(binaxis='y', stackdir='center', fill = "#999999") +
  stat_summary(fun.data="mean_sdl",  fun.args = list(mult=1))

Create a Dot Plot with multiple groups

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

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

# Change dots fill color by groups
e + geom_boxplot(width = 0.5) +
  geom_dotplot(aes(fill = supp), binaxis='y', stackdir='center')+
  scale_fill_manual(values = c("#00AFBB", "#E7B800"))

# Change the position : interval between dot plot of the same group
e + geom_boxplot(aes(color = supp), width = 0.5, position = position_dodge(0.8)) +
  geom_dotplot(aes(fill = supp, color = supp), binaxis='y', stackdir='center', 
               dotsize = 0.8,position = position_dodge(0.8))+
  scale_fill_manual(values = c("#00AFBB", "#E7B800"))+
  scale_color_manual(values = c("#00AFBB", "#E7B800"))

Conclusion

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