R Graphics Essentials for Great Data Visualization

Alboukadel KASSAMBARA
ii

Copyright ©2017 by Alboukadel Kassambara. All rights reserved.

Published by STHDA (http://www.sthda.com), Alboukadel Kassambara

Contact: Alboukadel Kassambara <[email protected]>

No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form
or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, without the prior
written permission of the Publisher. Requests to the Publisher for permission should
be addressed to STHDA (http://www.sthda.com).

Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in
preparing this book, they make no representations or warranties with respect to the accuracy or
completeness of the contents of this book and specifically disclaim any implied warranties of
merchantability or fitness for a particular purpose. No warranty may be created or extended by sales
representatives or written sales materials.

Neither the Publisher nor the authors, contributors, or editors,

assume any liability for any injury and/or damage
to persons or property as a matter of products liability,
negligence or otherwise, or from any use or operation of any
methods, products, instructions, or ideas contained in the material herein.

For general information contact Alboukadel Kassambara <[email protected]>.

Contents

0.1 What you will learn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vi

0.2 Book website . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vi
0.3 Executing the R codes from the PDF . . . . . . . . . . . . . . . . . . . . vi
0.4 Colophon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

About the author viii

1 R Basics for Data Visualization 1

1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Install R and RStudio . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.3 Install and load required R packages . . . . . . . . . . . . . . . . . . . . 2
1.4 Data format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.5 Import your data in R . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.6 Demo data sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.7 Data manipulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.8 R graphics systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.9 Export R graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

2 Plot One Variable 15

2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.2 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.3 One categorical variable . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.4 One continuous variable . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.5 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

3 Plot Grouped Data 37

3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.2 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.3 Grouped categorical variables . . . . . . . . . . . . . . . . . . . . . . . . 37
3.4 Grouped continuous variables . . . . . . . . . . . . . . . . . . . . . . . . 43
3.5 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
3.6 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

4 Plot Two Continuous Variables 68

4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
4.2 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
4.3 Basic scatter plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
4.4 Multiple groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
4.5 Add point text labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

iii
iv CONTENTS

4.6 Bubble chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

4.7 Color by a continuous variable . . . . . . . . . . . . . . . . . . . . . . . . 77
4.8 Add marginal density plots . . . . . . . . . . . . . . . . . . . . . . . . . 78
4.9 Continuous bivariate distribution . . . . . . . . . . . . . . . . . . . . . . 80
4.10 Zoom in a scatter plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
4.11 Add trend lines and equations . . . . . . . . . . . . . . . . . . . . . . . . 82
4.12 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
4.13 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

5 Plot Multivariate Continuous Data 86

5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
5.2 Demo data set and R package . . . . . . . . . . . . . . . . . . . . . . . . 86
5.3 Create a 3d scatter plot . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
5.4 Create a scatter plot matrix . . . . . . . . . . . . . . . . . . . . . . . . . 87
5.5 Correlation analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
5.6 Principal component analysis . . . . . . . . . . . . . . . . . . . . . . . . 91
5.7 Cluster analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
5.8 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

6 Visualizing Multivariate Categorical Data 95

6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
6.2 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
6.3 Bar plots of contingency tables . . . . . . . . . . . . . . . . . . . . . . . 95
6.4 Balloon plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
6.5 Mosaic plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
6.6 Correspondence analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 99

7 Plot Time Series Data 101

7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
7.2 Basic ggplot of time series . . . . . . . . . . . . . . . . . . . . . . . . . . 101
7.3 Plot multiple time series data . . . . . . . . . . . . . . . . . . . . . . . . 102
7.4 Set date axis limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
7.5 Format date axis labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
7.6 Add trend smoothed line . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
7.7 ggplot2 extensions for ts objects . . . . . . . . . . . . . . . . . . . . . . . 105

8 Facets: Multi-Panels GGPlot 108

8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
8.2 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
8.3 Split the plot into a matrix of panels . . . . . . . . . . . . . . . . . . . . 109
8.4 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112

9 Arrange Multiple GGPlot on One Page 113

9.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
9.2 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
9.3 Arrange on one page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
9.4 Annotate the arranged figure . . . . . . . . . . . . . . . . . . . . . . . . 114
9.5 Change column and row span of a plot . . . . . . . . . . . . . . . . . . . 115
9.6 Use shared legend for combined ggplots . . . . . . . . . . . . . . . . . . . 116
CONTENTS v

9.7 Mix table, text and ggplot2 graphs . . . . . . . . . . . . . . . . . . . . . 117

9.8 Arrange over multiple pages . . . . . . . . . . . . . . . . . . . . . . . . . 118
9.9 Export the arranged plots . . . . . . . . . . . . . . . . . . . . . . . . . . 119
9.10 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119

10 Customize GGPlot 120

10.1 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
10.2 Titles and axis labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
10.3 Axes: Limits, Ticks and Log . . . . . . . . . . . . . . . . . . . . . . . . . 122
10.4 Legends: Title, Position and Appearance . . . . . . . . . . . . . . . . . . 127
10.5 Themes gallery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
10.6 Background color and grid lines . . . . . . . . . . . . . . . . . . . . . . . 131
10.7 Add background image to ggplot2 graphs . . . . . . . . . . . . . . . . . . 132
10.8 Colors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
10.9 Points shape, color and size . . . . . . . . . . . . . . . . . . . . . . . . . 138
10.10Line types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
10.11Rotate a ggplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
10.12Plot annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
Preface

0.1 What you will learn

Data visualization is one of the most important part of data science. Many books and
courses present a catalogue of graphics but they don’t teach you which charts to use
according to the type of the data.
In this book, we start by presenting the key graphic systems and packages available in
R, including R base graphs, lattice and ggplot2 plotting systems.
Next, we provide practical examples to create great graphics for the right data using
either the ggplot2 package and extensions or the traditional R graphics.
With this book, you ’ll learn:
• How to quickly create beautiful graphics using ggplot2 packages
• How to properly customize and annotate the plots
• Type of graphics for visualizing categorical and continuous variables
• How to add automatically p-values to box plots, bar plots and alternatives
• How to add marginal density plots and correlation coefficients to scatter plots
• Key methods for analyzing and visualizing multivariate data
• R functions and packages for plotting time series data
• How to combine multiple plots on one page to create production-quality figures.

0.2 Book website

The website for this book is located at : http://www.sthda.com/english/. It contains
number of resources.

0.3 Executing the R codes from the PDF

For a single line R code, you can just copy the code from the PDF to the R console.

vi
0.4. COLOPHON vii

For a multiple-line R codes, an error is generated, sometimes, when you copy and paste
directly the R code from the PDF to the R console. If this happens, a solution is to:
• Paste firstly the code in your R code editor or in your text editor
• Copy the code from your text/code editor to the R console

0.4 Colophon
This book was built with R 3.3.2 and the following packages :
## name version source
## 1 bookdown 0.5 Github:rstudio/bookdown
## 2 changepoint 2.2.2 CRAN
## 3 cowplot 0.8.0.9000 Github:wilkelab/cowplot
## 4 dplyr 0.7.4 cran
## 5 factoextra 1.0.5.999 local:kassambara/factoextra
## 6 FactoMineR 1.38 CRAN
## 7 GGally 1.3.0 CRAN
## 8 ggcorrplot 0.1.1.9000 Github:kassambara/ggcorrplot
## 9 ggforce 0.1.1 Github:thomasp85/ggforce
## 10 ggformula 0.6 CRAN
## 11 ggfortify 0.4.1 CRAN
## 12 ggpmisc 0.2.15 CRAN
## 13 ggpubr 0.1.5.999 Github:kassambara/ggpubr
## 14 lattice 0.20-34 CRAN
## 15 readr 1.1.1 cran
## 16 scatterplot3d 0.3-40 cran
## 17 strucchange 1.5-1 CRAN
## 18 tidyr 0.7.2 cran
About the author

Alboukadel Kassambara is a PhD in Bioinformatics and Cancer Biology. He works

since many years on genomic data analysis and visualization (read more: http://www.
alboukadel.com/).
He has work experiences in statistical and computational methods to identify prognostic
and predictive biomarker signatures through integrative analysis of large-scale genomic
and clinical data sets.
He created a bioinformatics web-tool named GenomicScape (www.genomicscape.com)
which is an easy-to-use web tool for gene expression data analysis and visualization.
He developed also a training website on data science, named STHDA (Statistical Tools for
High-throughput Data Analysis, www.sthda.com/english), which contains many tutorials
on data analysis and visualization using R software and packages.
He is the author of many popular R packages for:
• multivariate data analysis (factoextra, http://www.sthda.com/english/rpkgs/
factoextra),
• survival analysis (survminer, http://www.sthda.com/english/rpkgs/
survminer/),
• correlation analysis (ggcorrplot, http://www.sthda.com/english/wiki/
ggcorrplot-visualization-of-a-correlation-matrix-using-ggplot2),
• creating publication ready plots in R (ggpubr, http://www.sthda.com/english/
rpkgs/ggpubr).
Recently, he published three books on data analysis and visualization:
1. Practical Guide to Cluster Analysis in R (https://goo.gl/yhhpXh)
2. Practical Guide To Principal Component Methods in R (https://goo.gl/d4Doz9)

viii
Chapter 1

R Basics for Data Visualization

1.1 Introduction
R is a free and powerful statistical software for analyzing and visualizing data.
In this chapter, you’ll learn:
• the basics of R programming for importing and manipulating your data:
– filtering and ordering rows,
– renaming and adding columns,
– computing summary statistics
• R graphics systems and packages for data visualization:
– R traditional base plots
– Lattice plotting system that aims to improve on R base graphics
– ggplot2 package, a powerful and a flexible R package, for producing elegant
graphics piece by piece.
– ggpubr package, which facilitates the creation of beautiful ggplot2-based
graphs for researcher with non-advanced programming backgrounds.
– ggformula package, an extension of ggplot2, based on formula interfaces (much
like the lattice interface)

1.2 Install R and RStudio

RStudio is an integrated development environment for R that makes using R easier. R
and RStudio can be installed on Windows, MAC OSX and Linux platforms.
1. R can be downloaded and installed from the Comprehensive R Archive Network
(CRAN) webpage (http://cran.r-project.org/)
2. After installing R software, install also the RStudio software available at: http:
//www.rstudio.com/products/RStudio/.
3. Launch RStudio and start use R inside R studio.

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2 CHAPTER 1. R BASICS FOR DATA VISUALIZATION

1.3 Install and load required R packages

An R package is a collection of functionalities that extends the capabilities of base R. To
use the R code provide in this book, you should install the following R packages:
• tidyverse packages, which are a collection of R packages that share the same
programming philosophy. These packages include:
– readr: for importing data into R
– dplyr: for data manipulation
– ggplot2 and ggpubr for data visualization.
• ggpubr package, which makes it easy, for beginner, to create publication ready
plots.
1. Install the tidyverse package. Installing tidyverse will install automatically
readr, dplyr, ggplot2 and more. Type the following code in the R console:
install.packages("tidyverse")

2. Install the ggpubr package.

• We recommend to install the latest developmental version of ggpubr as follow:
if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/ggpubr")

• If the above R code fails, you can install the latest stable version on CRAN:
install.packages("ggpubr")

3. Load required packages. After installation, you must first load the package for
using the functions in the package. The function library() is used for this task.
An alternative function is require(). For example, to load ggplot2 and ggpubr
packages, type this:
library("ggplot2")
library("ggpubr")

Now, we can use R functions, such as ggscatter() [in the ggpubr package] for creating a
scatter plot.
If you want to learn more about a given function, say ggscatter(), type this in R console:
?ggscatter.

1.4 Data format

Your data should be in rectangular format, where columns are variables and rows are
observations (individuals or samples).
• Column names should be compatible with R naming conventions. Avoid column
with blank space and special characters. Good column names: long_jump or
long.jump. Bad column name: long jump.
1.5. IMPORT YOUR DATA IN R 3

• Avoid beginning column names with a number. Use letter instead. Good column
names: sport_100m or x100m. Bad column name: 100m.
• Replace missing values by NA (for not available)
For example, your data should look like this:
manufacturer model displ year cyl trans drv
1 audi a4 1.8 1999 4 auto(l5) f
2 audi a4 1.8 1999 4 manual(m5) f
3 audi a4 2.0 2008 4 manual(m6) f
4 audi a4 2.0 2008 4 auto(av) f
Read more at: Best Practices in Preparing Data Files for Importing into R1

1.5 Import your data in R

First, save your data into txt or csv file formats and import it as follow (you will be asked
to choose the file):
library("readr")

# Reads tab delimited files (.txt tab)

my_data <- read_tsv(file.choose())

# Reads comma (,) delimited files (.csv)

my_data <- read_csv(file.choose())

# Reads semicolon(;) separated files(.csv)

my_data <- read_csv2(file.choose())

Read more about how to import data into R at this link: http://www.sthda.com/
english/wiki/importing-data-into-r

1.6 Demo data sets

R comes with several demo data sets for playing with R functions. The most used R
demo data sets include: USArrests, iris and mtcars. To load a demo data set, use the
function data() as follow. The function head() is used to inspect the data.
data("iris") # Loading
head(iris, n = 3) # Print the first n = 3 rows

## Sepal.Length Sepal.Width Petal.Length Petal.Width Species

## 1 5.1 3.5 1.4 0.2 setosa
## 2 4.9 3.0 1.4 0.2 setosa
1
http://www.sthda.com/english/wiki/best-practices-in-preparing-data-files-for-
importing-into-r
4 CHAPTER 1. R BASICS FOR DATA VISUALIZATION

## 3 4.7 3.2 1.3 0.2 setosa

To learn more about iris data sets, type this:
?iris

After typing the above R code, you will see the description of iris data set: this iris
data set gives the measurements in centimeters of the variables sepal length and width
and petal length and width, respectively, for 50 flowers from each of 3 species of iris. The
species are Iris setosa, versicolor, and virginica.

1.7 Data manipulation

After importing your data in R, you can easily manipulate it using the dplyr package
(Wickham et al., 2017), which can be installed using the R code: install.packages("dplyr").
After loading dplyr, you can use the following R functions:
• filter(): Pick rows (observations/samples) based on their values.
• distinct(): Remove duplicate rows.
• arrange(): Reorder the rows.
• select(): Select columns (variables) by their names.
• rename(): Rename columns.
• mutate(): Add/create new variables.
• summarise(): Compute statistical summaries (e.g., computing the mean or the
sum)
• group_by(): Operate on subsets of the data set.

Note that, dplyr package allows to use the forward-pipe chaining operator (%>%) for
combining multiple operations. For example, x %>% f is equivalent to f(x). Using
the pipe (%>%), the output of each operation is passed to the next operation. This
makes R programming easy.

We’ll show you how these functions work in the different chapters of this book.

1.8 R graphics systems

There are different graphic packages available in R2 for visualizing your data: 1) R base
graphs, 2) Lattice Graphs (Sarkar, 2016) and 3) ggplot2 (Wickham and Chang, 2017).
In this section, we start by providing a quick overview of R base and lattice plots, and
then we move to ggplot2 graphic system. The vast majority of plots generated in this
book is based on the modern and flexible ggplot2 R package.
2
http://www.sthda.com/english/wiki/data-visualization
1.8. R GRAPHICS SYSTEMS 5

1.8.1 R base graphs

R comes with simple functions to create many types of graphs. For example:

Plot Types R base function

Scatter plot plot()
Scatter plot matrix pairs()
Box plot boxplot()
Strip chart stripchart()
Histogram plot hist()
density plot density()
Bar plot barplot()
Line plot plot() and line()
Pie charts pie()
Dot charts dotchart()
Add text to a plot text()

In the most cases, you can use the following arguments to customize the plot:
• pch: change point shapes. Allowed values comprise number from 1 to 25.
• cex: change point size. Example: cex = 0.8.
• col: change point color. Example: col = “blue”.
• frame: logical value. frame = FALSE removes the plot panel border frame.
• main, xlab, ylab. Specify the main title and the x/y axis labels -, respectively
• las: For a vertical x axis text, use las = 2.
In the following R code, we’ll use the iris data set to create a:
• (1) Scatter plot of Sepal.Length (on x-axis) and Sepal.Width (on y-axis).
• (2) Box plot of Sepal.length (y-axis) by Species (x-axis)
# (1) Create a scatter lot
plot(
x = iris$Sepal.Length, y = iris$Sepal.Width,
pch = 19, cex = 0.8, frame = FALSE,
xlab = "Sepal Length",ylab = "Sepal Width"
)

# (2) Create a box plot

boxplot(Sepal.Length ~ Species, data = iris,
ylab = "Sepal.Length",
frame = FALSE, col = "lightgray")
6 CHAPTER 1. R BASICS FOR DATA VISUALIZATION

2.0 2.5 3.0 3.5 4.0

Sepal Width

7.5
Sepal.Length

6.5
5.5
4.5
4.5 5.5 6.5 7.5

Sepal Length setosa virginica

Read more examples at: R base Graphics on STHDA, http://www.sthda.com/
english/wiki/r-base-graphs

1.8.2 Lattice graphics

The lattice R package provides a plotting system that aims to improve on R base graphs.
After installing the package, whith the R command install.packages("lattice"), you
can test the following functions.
• Main functions in the lattice package:

Plot types Lattice functions

Scatter plot xyplot()
Scatter plot matrix splom()
3D scatter plot cloud()
Box plot bwplot()
strip plots (1-D scatter plots) stripplot()
Dot plot dotplot()
Bar chart barchart()
Histogram histogram()
Density plot densityplot()
Theoretical quantile plot qqmath()
Two-sample quantile plot qq()
3D contour plot of surfaces contourplot()
False color level plot of surfaces levelplot()
Parallel coordinates plot parallel()
3D wireframe graph wireframe()

The lattice package uses formula interface. For example, in lattice terminology, the
formula y ~ x | group, means that we want to plot the y variable according to the x
variable, splitting the plot into multiple panels by the variable group.
1.8. R GRAPHICS SYSTEMS 7

• Create a basic scatter plot of y by x. Syntax: y ~ x. Change the color by

groups and use auto.key = TRUE to show legends:
library("lattice")
xyplot(
Sepal.Length ~ Petal.Length, group = Species,
data = iris, auto.key = TRUE, pch = 19, cex = 0.5
)
setosa
versicolor
virginica

8
Sepal.Length

1 2 3 4 5 6 7

Petal.Length

• Multiple panel plots by groups. Syntax: y ~ x | group.

xyplot(
Sepal.Length ~ Petal.Length | Species,
layout = c(3, 1), # panel with ncol = 3 and nrow = 1
group = Species, data = iris,
type = c("p", "smooth"), # Show points and smoothed line
scales = "free" # Make panels axis scales independent
)

setosa versicolor virginica

5.0 5.5 6.0 6.5 7.0 7.5 8.0
7.0
5.5
Sepal.Length

6.5
6.0
5.0

5.5
4.5

5.0

1.0 1.2 1.4 1.6 1.8 3.0 3.5 4.0 4.5 5.0 4.5 5.0 5.5 6.0 6.5 7.0

Petal.Length

Read more examples at: Lattice Graphics on STHDAa

a
http://www.sthda.com/english/wiki/lattice-graphs
8 CHAPTER 1. R BASICS FOR DATA VISUALIZATION

1.8.3 ggplot2 graphics

GGPlot2 is a powerful and a flexible R package, implemented by Hadley Wickham,

for producing elegant graphics piece by piece. The gg in ggplot2 means Grammar of
Graphics, a graphic concept which describes plots by using a “grammar”. According to
the ggplot2 concept, a plot can be divided into different fundamental parts: Plot = data
+ Aesthetics + Geometry
• data: a data frame
• aesthetics: used to indicate the x and y variables. It can be also used to control
the color, the size and the shape of points, etc…..
• geometry: corresponds to the type of graphics (histogram, box plot, line plot, ….)

The ggplot2 syntax might seem opaque for beginners, but once you understand the
basics, you can create and customize any kind of plots you want.
Note that, to reduce this opacity, we recently created an R package, named ggpubr
(ggplot2 Based Publication Ready Plots), for making ggplot simpler for students and
researchers with non-advanced programming backgrounds. We’ll present ggpubr in
the next section.

After installing and loading the ggplot2 package, you can use the following key functions:

Plot types GGPlot2 functions

Initialize a ggplot ggplot()
Scatter plot geom_point()
Box plot geom_boxplot()
Violin plot geom_violin()
strip chart geom_jitter()
Dot plot geom_dotplot()
Bar chart geom_bar()
Line plot geom_line()
Histogram geom_histogram()
Density plot geom_density()
Error bars geom_errorbar()
QQ plot stat_qq()
ECDF plot stat_ecdf()
Title and axis labels labs()

The main function in the ggplot2 package is ggplot(), which can be used to initialize
the plotting system with data and x/y variables.
For example, the following R code takes the iris data set to initialize the ggplot and
then a layer (geom_point()) is added onto the ggplot to create a scatter plot of x =
Sepal.Length by y = Sepal.Width:
library(ggplot2)
ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width))+
geom_point()
1.8. R GRAPHICS SYSTEMS 9

# Change point size, color and shape

ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width))+
geom_point(size = 1.2, color = "steelblue", shape = 21)
4.5 4.5

4.0 4.0
Sepal.Width

Sepal.Width
3.5 3.5

3.0 3.0

2.5 2.5

2.0 2.0
5 6 7 8 5 6 7 8
Sepal.Length Sepal.Length

Note that, in the code above, the shape of points is specified as number. To display the
different point shape available in R, type this:
ggpubr::show_point_shapes()

It’s also possible to control points shape and color by a grouping variable (here, Species).
For example, in the code below, we map points color and shape to the Species grouping
variable.
# Control points color by groups
ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width))+
geom_point(aes(color = Species, shape = Species))

# Change the default color manually.

# Use the scale_color_manual() function
ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width))+
geom_point(aes(color = Species, shape = Species))+
scale_color_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))
10 CHAPTER 1. R BASICS FOR DATA VISUALIZATION

4.5 4.5

4.0 4.0

Species Species
Sepal.Width

Sepal.Width
3.5 3.5
setosa setosa

3.0 versicolor 3.0 versicolor

virginica virginica
2.5 2.5

2.0 2.0
5 6 7 8 5 6 7 8
Sepal.Length Sepal.Length

You can also split the plot into multiple panels according to a grouping variable. R
function: facet_wrap(). Another interesting feature of ggplot2, is the possibility to
combine multiple layers on the same plot. For example, with the following R code, we’ll:
• Add points with geom_point(), colored by groups.
• Add the fitted smoothed regression line using geom_smooth(). By default the
function geom_smooth() add the regression line and the confidence area. You can
control the line color and confidence area fill color by groups.
• Facet the plot into multiple panels by groups
• Change color and fill manually using the function scale_color_manual() and
scale_fill_manual()
ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width))+
geom_point(aes(color = Species))+
geom_smooth(aes(color = Species, fill = Species))+
facet_wrap(~Species, ncol = 3, nrow = 1)+
scale_color_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))+
scale_fill_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))

setosa versicolor virginica

4.5

4.0
Species
Sepal.Width

3.5
setosa

3.0 versicolor
virginica
2.5

2.0

5 6 7 8 5 6 7 8 5 6 7 8
Sepal.Length

Note that, the default theme of ggplots is theme_gray() (or theme_grey()), which is
theme with grey background and white grid lines. More themes are available for profes-
sional presentations or publications. These include: theme_bw(), theme_classic() and
1.8. R GRAPHICS SYSTEMS 11

theme_minimal().
To change the theme of a given ggplot (p), use this: p + theme_classic(). To change
the default theme to theme_classic() for all the future ggplots during your entire R
session, type the following R code:
theme_set(
theme_classic()
)

Now you can create ggplots with theme_classic() as default theme:

ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width))+
geom_point()
4.5

4.0
Sepal.Width

3.5

3.0

2.5

2.0
5 6 7 8
Sepal.Length

1.8.4 ggpubr for publication ready plots

The ggpubr R package facilitates the creation of beautiful ggplot2-based graphs for
researcher with non-advanced programming backgrounds (Kassambara, 2017).
For example, to create the density distribution of “Sepal.Length”, colored by groups
(“Species”), type this:
library(ggpubr)
# Density plot with mean lines and marginal rug
ggdensity(iris, x = "Sepal.Length",
add = "mean", rug = TRUE, # Add mean line and marginal rugs
color = "Species", fill = "Species", # Color by groups
palette = "jco") # use jco journal color palette
12 CHAPTER 1. R BASICS FOR DATA VISUALIZATION

Species setosa versicolor virginica

1.2

0.8
density

0.4

0.0
5 6 7 8
Sepal.Length

Note that the argument palette can take also a custom color palette. For example
palette= c("#00AFBB", "#E7B800", "#FC4E07").

• Create a box plot with p-values comparing groups:

# Groups that we want to compare
my_comparisons <- list(
c("setosa", "versicolor"), c("versicolor", "virginica"),
c("setosa", "virginica")
)

# Create the box plot. Change colors by groups: Species

# Add jitter points and change the shape by groups
ggboxplot(
iris, x = "Species", y = "Sepal.Length",
color = "Species", palette = c("#00AFBB", "#E7B800", "#FC4E07"),
add = "jitter"
)+
stat_compare_means(comparisons = my_comparisons, method = "t.test")
1.9. EXPORT R GRAPHICS 13

Species setosa versicolor virginica

9 < 2.2e-16
1.9e-07
< 2.2e-16
8
Sepal.Length

setosa versicolor virginica

Species

Learn more on STHDA at: ggpubr: Publication Ready Plotsa

a
http://www.sthda.com/english/articles/24-ggpubr-publication-ready-plots/

1.9 Export R graphics

You can export R graphics to many file formats, including: PDF, PostScript, SVG vector
files, Windows MetaFile (WMF), PNG, TIFF, JPEG, etc.
The standard procedure to save any graphics from R is as follow:
1. Open a graphic device using one of the following functions:
• pdf(“r-graphics.pdf”),
• postscript(“r-graphics.ps”),
• svg(“r-graphics.svg”),
• png(“r-graphics.png”),
• tiff(“r-graphics.tiff”),
• jpeg(“r-graphics.jpg”),
• win.metafile(“r-graphics.wmf”),
• and so on.
Additional arguments indicating the width and the height (in inches) of the graphics
region can be also specified in the mentioned function.
2. Create a plot
3. Close the graphic device using the function dev.off()
For example, you can export R base plots to a pdf file as follow:
14 CHAPTER 1. R BASICS FOR DATA VISUALIZATION

pdf("r-base-plot.pdf")
# Plot 1 --> in the first page of PDF
plot(x = iris$Sepal.Length, y = iris$Sepal.Width)
# Plot 2 ---> in the second page of the PDF
hist(iris$Sepal.Length)
dev.off()

To export ggplot2 graphs, the R code looks like this:

# Create some plots
library(ggplot2)
myplot1 <- ggplot(iris, aes(Sepal.Length, Sepal.Width)) +
geom_point()
myplot2 <- ggplot(iris, aes(Species, Sepal.Length)) +
geom_boxplot()

# Print plots to a pdf file

pdf("ggplot.pdf")
print(myplot1) # Plot 1 --> in the first page of PDF
print(myplot2) # Plot 2 ---> in the second page of the PDF
dev.off()

Note that for a ggplot, you can also use the following functions to export the graphic:
• ggsave() [in ggplot2]. Makes it easy to save a ggplot. It guesses the type of
graphics device from the file extension.
• ggexport() [in ggpubr]. Makes it easy to arrange and export multiple ggplots at
once.
See also the following blog post to save high-resolution ggplotsa
a
http://www.sthda.com/english/wiki/saving-high-resolution-ggplots-how-to-
preserve-semi-transparency
Chapter 2

Plot One Variable

2.1 Introduction
To visualize one variable, the type of graphs to be used depends on the type of the
variable:
• For categorical variable or grouping variables. You can visualize the count of
categories using a bar plot or using a pie chart to show the proportion of each
category.
• For continuous variable, you can visualize the distribution of the variable using
density plots, histograms and alternatives.
In this R graphics tutorial, you’ll learn how to:
• Visualize a categorical variable using bar plots, dot charts and pie charts
• Visualize the distribution of a continuous variable using:
– density and histogram plots,
– other alternatives, such as frequency polygon, area plots, dot plots, box plots,
Empirical cumulative distribution function (ECDF) and Quantile-quantile plot
(QQ plots).
– Density ridgeline plots, which are useful for visualizing changes in distributions,
of a continuous variable, over time or space.
– Bar plot and modern alternatives, including lollipop charts and cleveland’s
dot plots.

2.2 Prerequisites
Load required packages and set the theme function theme_pubr() [in ggpubr] as the
default theme:
library(ggplot2)
library(ggpubr)
theme_set(theme_pubr())

15
16 CHAPTER 2. PLOT ONE VARIABLE

2.3 One categorical variable

2.3.1 Bar plot of counts

• Plot types: Bar plot of the count of group levels

• Key function: geom_bar()
• Key arguments: alpha, color, fill, linetype and size
Demo data set: diamonds [in ggplot2]. Contains the prices and other attributes of almost
54000 diamonds. The column cut contains the quality of the diamonds cut (Fair, Good,
Very Good, Premium, Ideal).
The R code below creates a bar plot visualizing the number of elements in each category
of diamonds cut.
ggplot(diamonds, aes(cut)) +
geom_bar(fill = "#0073C2FF") +
theme_pubclean()

20000

15000
count

10000

5000

0
Fair Good Very Good Premium Ideal
cut
Compute the frequency of each category and add the labels on the bar plot:
• dplyr package used to summarise the data
• geom_bar() with option stat = "identity" is used to create the bar plot of the
summary output as it is.
• geom_text() used to add text labels. Adjust the position of the labels by using
hjust (horizontal justification) and vjust (vertical justification). Values should be
in [0, 1].
# Compute the frequency
library(dplyr)
df <- diamonds %>%
group_by(cut) %>%
summarise(counts = n())
df

## # A tibble: 5 x 2
## cut counts
## <ord> <int>
2.3. ONE CATEGORICAL VARIABLE 17

## 1 Fair 1610
## 2 Good 4906
## 3 Very Good 12082
## 4 Premium 13791
## 5 Ideal 21551
# Create the bar plot. Use theme_pubclean() [in ggpubr]
ggplot(df, aes(x = cut, y = counts)) +
geom_bar(fill = "#0073C2FF", stat = "identity") +
geom_text(aes(label = counts), vjust = -0.3) +
theme_pubclean()
21551
20000

15000 13791
12082
counts

10000

5000
4906

1610
0
Fair Good Very Good Premium Ideal
cut

2.3.2 Pie charts

Pie chart is just a stacked bar chart in polar coordinates.

First,
• Arrange the grouping variable (cut) in descending order. This important to com-
pute the y coordinates of labels.
• compute the proportion (counts/total) of each category
• compute the position of the text labels as the cumulative sum of the proportion. To
put the labels in the center of pies, we’ll use cumsum(prop) - 0.5*prop as label
position.
df <- df %>%
arrange(desc(cut)) %>%
mutate(prop = round(counts*100/sum(counts), 1),
lab.ypos = cumsum(prop) - 0.5*prop)
head(df, 4)

## # A tibble: 4 x 4
## cut counts prop lab.ypos
18 CHAPTER 2. PLOT ONE VARIABLE

## <ord> <int> <dbl> <dbl>

## 1 Ideal 21551 40.0 20.0
## 2 Premium 13791 25.6 52.8
## 3 Very Good 12082 22.4 76.8
## 4 Good 4906 9.1 92.5
• Create the pie charts using ggplot2 verbs. Key function: coord_polar().
ggplot(df, aes(x = "", y = prop, fill = cut)) +
geom_bar(width = 1, stat = "identity", color = "white") +
geom_text(aes(y = lab.ypos, label = prop), color = "white")+
coord_polar("y", start = 0)+
ggpubr::fill_palette("jco")+
theme_void()

cut
9.1 3
Fair
40 Good
22.4
Very Good
Premium

25.6 Ideal

• Alternative solution to easily create a pie chart: use the function ggpie()[in gg-
pubr]:
ggpie(
df, x = "prop", label = "prop",
lab.pos = "in", lab.font = list(color = "white"),
fill = "cut", color = "white",
palette = "jco"
)

2.3.3 Dot charts

Dot chart is an alternative to bar plots. Key functions:

• geom_linerange():Creates line segments from x to ymax
• geom_point(): adds dots
• ggpubr::color_palette(): changes color palette.
ggplot(df, aes(cut, prop)) +
geom_linerange(
aes(x = cut, ymin = 0, ymax = prop),
color = "lightgray", size = 1.5
2.4. ONE CONTINUOUS VARIABLE 19

)+
geom_point(aes(color = cut), size = 2)+
ggpubr::color_palette("jco")+
theme_pubclean()

cut Fair Good Very Good Premium Ideal

40

30
prop

20

10

0
Fair Good Very Good Premium Ideal
cut
Easy alternative to create a dot chart. Use ggdotchart() [ggpubr]:
ggdotchart(
df, x = "cut", y = "prop",
color = "cut", size = 3, # Points color and size
add = "segment", # Add line segments
add.params = list(size = 2),
palette = "jco",
ggtheme = theme_pubclean()
)

2.4 One continuous variable

Different types of graphs can be used to visualize the distribution of a continuous variable,
including: density and histogram plots.

2.4.1 Data format

Create some data (wdata) containing the weights by sex (M for male; F for female):
set.seed(1234)
wdata = data.frame(
sex = factor(rep(c("F", "M"), each=200)),
weight = c(rnorm(200, 55), rnorm(200, 58))
)

head(wdata, 4)