ggplot2 box plot : Quick start guide - R software and data visualization

This R tutorial describes how to create a box plot using R software and ggplot2 package.

The function geom_boxplot() is used. A simplified format is :

geom_boxplot(outlier.colour="black", outlier.shape=16, outlier.size=2, notch=FALSE)

outlier.colour, outlier.shape, outlier.size : The color, the shape and the size for outlying points
notch : logical value. If TRUE, make a notched box plot. The notch displays a confidence interval around the median which is normally based on the median +/- 1.58*IQR/sqrt(n). Notches are used to compare groups; if the notches of two boxes do not overlap, this is a strong evidence that the medians differ.

Prepare the data

ToothGrowth data sets are used :

# Convert the variable dose from a numeric to a factor variable ToothGrowth$dose


## 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 ## 5 6.4 VC 0.5 ## 6 10.0 VC 0.5
Make sure that the variable dose is converted as a factor variable using the above R script.
Basic box plots
library(ggplot2) # Basic box plot p 


The function stat_summary() can be used to add mean points to a box plot :
# Box plot with mean points p + stat_summary(fun.y=mean, geom="point", shape=23, size=4)

Choose which items to display :
p + scale_x_discrete(limits=c("0.5", "2"))

Box plot with dots
Dots (or points) can be added to a box plot using the functions geom_dotplot() or geom_jitter() :
# Box plot with dot plot p + geom_dotplot(binaxis='y', stackdir='center', dotsize=1) # Box plot with jittered points # 0.2 : degree of jitter in x direction p + geom_jitter(shape=16, position=position_jitter(0.2))

Change box plot colors by groups
Change box plot line colors
Box plot line colors can be automatically controlled by the levels of the variable dose :
# Change box plot line colors by groups p<-ggplot(ToothGrowth, aes(x=dose, y=len, color=dose)) + geom_boxplot() p

It is also possible to change manually box plot line colors using the functions :

  scale_color_manual() : to use custom colors
  scale_color_brewer() : to use color palettes from RColorBrewer package
  scale_color_grey() : to use grey color palettes

# Use custom color palettes p+scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9")) # Use brewer color palettes p+scale_color_brewer(palette="Dark2") # Use grey scale p + scale_color_grey() + theme_classic()

Read more on ggplot2 colors here : ggplot2 colors
Change box plot fill colors
In the R code below, box plot fill colors are automatically controlled by the levels of dose :
# Use single color ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_boxplot(fill='#A4A4A4', color="black")+ theme_classic() # Change box plot colors by groups p<-ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose)) + geom_boxplot() p

It is also possible to change manually box plot fill colors using the functions :

  scale_fill_manual() : to use custom colors
  scale_fill_brewer() : to use color palettes from RColorBrewer package
  scale_fill_grey() : to use grey color palettes

# Use custom color palettes p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9")) # use brewer color palettes p+scale_fill_brewer(palette="Dark2") # Use grey scale p + scale_fill_grey() + theme_classic()

Read more on ggplot2 colors here : ggplot2 colors
Change the legend position
p + theme(legend.position="top") p + theme(legend.position="bottom") p + theme(legend.position="none") # Remove legend

The allowed values for the arguments legend.position are : “left”,“top”, “right”, “bottom”.
Read more on ggplot legend : ggplot2 legend
Change the order of items in the legend
The function scale_x_discrete can be used to change the order of items to “2”, “0.5”, “1” :
p + scale_x_discrete(limits=c("2", "0.5", "1"))

Box plot with multiple groups
# Change box plot colors by groups ggplot(ToothGrowth, aes(x=dose, y=len, fill=supp)) + geom_boxplot() # Change the position p<-ggplot(ToothGrowth, aes(x=dose, y=len, fill=supp)) + geom_boxplot(position=position_dodge(1)) p

Change box plot colors and add dots :
# Add dots p + geom_dotplot(binaxis='y', stackdir='center', position=position_dodge(1)) # Change colors p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))

Customized box plots
# Basic box plot ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_boxplot(fill="gray")+ labs(title="Plot of length per dose",x="Dose (mg)", y = "Length")+ theme_classic() # Change automatically color by groups bp 


Change fill colors manually :
# Continuous colors bp + scale_fill_brewer(palette="Blues") + theme_classic() # Discrete colors bp + scale_fill_brewer(palette="Dark2") + theme_minimal() # Gradient colors bp + scale_fill_brewer(palette="RdBu") + theme_minimal()

Read more on ggplot2 colors here : ggplot2 colors
Infos
This analysis has been performed using R software (ver. 3.1.2) and ggplot2 (ver. 1.0.0)
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