Boxplots in Base R

Preliminary tasks

1. Launch RStudio as described here: Running RStudio and setting up your working directory

2. Prepare your data as described here: Best practices for preparing your data and save it in an external .txt tab or .csv files

3. Import your data into R as described here: Fast reading of data from txt|csv files into R: readr package.

Here, we'll use the R built-in ToothGrowth data set.

# Print the first 6 rows
head(ToothGrowth, 6)

##    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

Source: STHDA, http://www.sthda.com/english/wiki/box-plots-r-base-graphs
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License.

R base box plots: boxplot()

Draw a box plot of teeth length (len):

Basic box plots

# Box plot of one variable
boxplot(ToothGrowth$len)
# Box plots by groups (dose)
# remove frame
boxplot(len ~ dose, data = ToothGrowth, frame = FALSE)
# Horizontal box plots
boxplot(len ~ dose, data = ToothGrowth, frame = FALSE,
        horizontal = TRUE)
# Notched box plots
boxplot(len ~ dose, data = ToothGrowth, frame = FALSE,
        notch = TRUE)

Notch is used to compare groups. In the notched boxplot, if two boxes' notches do not overlap this is "strong evidence" their medians differ (Chambers et al., 1983, p. 62).

Change group names

boxplot(len ~ dose, data = ToothGrowth, frame = FALSE,
        names = c("D0.5", "D1", "D2"))

Change color

# Change the color of border using one single color
boxplot(len ~ dose, data = ToothGrowth, frame = FALSE,
        border = "steelblue")
# Change the color of border.
#  Use different colors for each group
boxplot(len ~ dose, data = ToothGrowth, frame = FALSE,
        border = c("#999999", "#E69F00", "#56B4E9"))
# Change fill color : single color
boxplot(len ~ dose, data = ToothGrowth, frame = FALSE,
        col = "steelblue")
# Change fill color: multiple colors
boxplot(len ~ dose, data = ToothGrowth, frame = FALSE,
        col = c("#999999", "#E69F00", "#56B4E9"))

Box plot with multiple groups

boxplot(len ~ supp*dose, data = ToothGrowth,
        col = c("white", "steelblue"), frame = FALSE)

Change main title and axis labels

# Change axis titles
# Change color (col = "gray") and remove frame
# Create notched box plot
boxplot(len ~ dose, data = ToothGrowth,
        main = "Plot of length by dose",
        xlab = "Dose (mg)", ylab = "Length",
        col = "lightgray", frame = FALSE)

Box plot with the number of observations: gplots::boxplot2()

The function boxplot2()[in gplots package] can be used to create a box plot annotated with the number of observations.

Install gplots:

install.packages("gplots")

Use boxplot2() [in gplots]:

library("gplots")
# Box plot with annotation
boxplot2(len ~ dose, data = ToothGrowth,
         frame = FALSE)

# Put the annotation at the top
boxplot2(len ~ dose, data = ToothGrowth,
         frame = FALSE, top = TRUE)

Summary

Create basic box plots

boxplot(len ~ dose, data = ToothGrowth, frame = FALSE)

Box plots with the number of observations

gplots::boxplot2(len ~ dose, data = ToothGrowth,
                 frame = FALSE, top = TRUE)