Box Plots - R Base Graphs


Previously, we described the essentials of R programming and provided quick start guides for importing data into R.


Here, we’ll describe how to create box plots in R.


Pleleminary 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

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

Infos

This analysis has been performed using R statistical software (ver. 3.2.4).


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