Create

Imagine Communi-
cate and
Transform
ggplot2, data Audience
visualization 1 2 3

Alboukadel Kassambara

Guide to Create
Beautiful Graphics in R

sthda.com Edition 21
A. Kassambara
2015
Order a physical copy from amazon at
https://goo.gl/Pz3Neg

A. Kassambara 2
2015
2

Copyright 2013 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]>.

0.1. PREFACE TO THE SECOND EDITION 3

0.1 Preface to the second edition

We have been gratified by the popularity of the first edition of ggplot2: the elements
for elegant data visualization in R. This, along with the release of the version 2.0 of
ggplot2 R package, motivated us to update our book with a second edition.
We have simplified several chapters, including quick plot, density plots, histogram
plots, ECDF plots and QQ plots. We have added new chapters and updated some of
the existing chapters. Here is a summary of the main changes:

1. New features added:

Introduction to R (chapter 1)
Area plot (chapter 3)
Frequency polygon (chapter 7)
Dot plot for one variable (chapter 8)
Scatter plot (chapter 12)
quantile line from quantile regression
jitter to reduce overplotting
Continuous bivariate distribution (chapter 13)
Correlation Matrix Visualization (chapter 41)
ggcorrplot: new R package for visualizing a correlation matrix
Line plot with time series data updated
Graphical parameters:
Position adjustements (chapter 38)
Coordinate systems (chapter 39)
Text annotations: ggrepel R package (chapter 34)
survminer: new R package for plotting survival curves with number at risk table
(chapter 42)

2. Removed sections:

Line plot
Add arrow section removed
Legend
Section remove legend slashes (not required since ggplot2 v2)
4

0.2 Preface to the first edition

ggplot2 is an R package implemented by Hadley Wickham for creating graphs.
Its based on the Grammar of Graphics, a concept published by Leland Wilkinson
in 2005.
ggplot2 has become a popular package for data visualization. The official documenta-
tion of the package is available at: http://docs.ggplot2.org/current/. However, going
through this comprehensive documentation can drive you crazy!
To make things easy and simple, well present, in this book, the most important
functions available in ggplot2 package to generate nice looking graphs. You will find
many examples of R codes and graphics in this document.

Note that, all the analyses in this book were performed using R (ver. 3.2.3) and
ggplot2 (ver 2.1.0).

0.3 Acknowledgments
Thanks to Leland Wilkinson for the concept,
Thanks to Hadley Wickham for ggplot2 R package

0.4 About the author

Alboukadel Kassambara is a PhD in Bioinformatics and Cancer Biology. He works since
many years on genomic data analysis and visualization. He created a bioinformatics
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 website
called STHDA (Statistical Tools for High-throughput Data Analysis, www.sthda.com),
which contains many tutorials on data analysis and visualization using R software
and packages. He is the author of the R packages survminer (for analyzing and
drawing survival curves), ggcorrplot (for drawing correlation matrix using ggplot2)
and factoextra (to easily extract and visualize the results of multivariate analysis
such PCA, CA, MCA and clustering).
Contents

0.1 Preface to the second edition . . . . . . . . . . . . . . . . . . . . . . . 3

0.2 Preface to the first edition . . . . . . . . . . . . . . . . . . . . . . . . 4
0.3 Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
0.4 About the author . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
0.5 How this book is organized? . . . . . . . . . . . . . . . . . . . . . . . 13
0.6 Book website . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
0.7 How to execute the R codes provided in this book? . . . . . . . . . . 18

I Basics of R and ggplot2 19

1 Introduction to R 20
1.1 Install R and RStudio . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.2 Arithmetics with R . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
1.3 Data types in R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
1.4 Getting help with functions in R . . . . . . . . . . . . . . . . . . . . . 24
1.5 Installing and loading R packages . . . . . . . . . . . . . . . . . . . . 24
1.6 Importing your data into R . . . . . . . . . . . . . . . . . . . . . . . 26
1.7 Demo data sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
1.8 Close your R/RStudio session . . . . . . . . . . . . . . . . . . . . . . 28

5
6 CONTENTS

2 Introduction to ggplot2 29
2.1 Whats ggplot2? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.2 Type of graphs for data visualization . . . . . . . . . . . . . . . . . . 30
2.3 Install and load ggplot2 package . . . . . . . . . . . . . . . . . . . . . 31
2.4 Data format and preparation . . . . . . . . . . . . . . . . . . . . . . . 31
2.5 qplot() function: Draw quick plots . . . . . . . . . . . . . . . . . . . . 32
2.6 ggplot() function: Build plots piece by piece . . . . . . . . . . . . . . 35
2.7 Save ggplots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

II Plot One Variable - X: Continuous or Discrete 40

2.8 Data format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
2.9 Plot types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

3 Area Plots 43

4 Density Plots 45
4.1 Basic density plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
4.2 Change colors by groups . . . . . . . . . . . . . . . . . . . . . . . . . 46

5 Histogram Plots 49
5.1 Basic histogram plots . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
5.2 Change colors by groups . . . . . . . . . . . . . . . . . . . . . . . . . 51

6 Combine Histogram and Density Plots 53

7 Frequency Polygon 54

8 Dot Plots for One Variable 56

9 ECDF Plots 57

10 QQ Plots 58
CONTENTS 7

11 Bar Plots of Counts 60

III Plot Two Variables - X & Y: Both Continuous or Dis-

crete 61

12 Scatter plots: Continuous X and Y 62

12.1 Data format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
12.2 Plot types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
12.3 Basic scatter plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
12.4 Scatter plots with multiple groups . . . . . . . . . . . . . . . . . . . . 65
12.5 Add regression line or smoothed conditional mean . . . . . . . . . . . 68
12.6 Add quantile lines from a quantile regression . . . . . . . . . . . . . . 71
12.7 Add marginal rugs to a scatter plot . . . . . . . . . . . . . . . . . . . 72
12.8 Jitter points to reduce overplotting . . . . . . . . . . . . . . . . . . . 73
12.9 Textual annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

13 Continuous bivariate distribution 75

13.1 Data format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
13.2 Plot types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
13.3 Add heatmap of 2d bin counts . . . . . . . . . . . . . . . . . . . . . . 76
13.4 Add hexagon bining . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
13.5 Scatter plots with 2d density estimation . . . . . . . . . . . . . . . . 79
13.6 Continuous function . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

14 Two variables: Discrete X, Discrete Y 82

IV Plot Two Variables - X & Y: Discrete X and Continu-

ous Y 84
14.1 Data format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
14.2 Plot types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
8 CONTENTS

15 Box Plots 87
15.1 Basic box plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
15.2 Change colors by groups . . . . . . . . . . . . . . . . . . . . . . . . . 89
15.3 Box plot with multiple groups . . . . . . . . . . . . . . . . . . . . . . 91

16 Violin plots 93
16.1 Basic violin plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
16.2 Add summary statistics . . . . . . . . . . . . . . . . . . . . . . . . . . 94
16.3 Change colors by groups . . . . . . . . . . . . . . . . . . . . . . . . . 95
16.4 Violin plots with multiple groups . . . . . . . . . . . . . . . . . . . . 96

17 Dot Plots 97
17.1 Basic dot plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
17.2 Add summary statistics . . . . . . . . . . . . . . . . . . . . . . . . . . 98
17.3 Change colors by groups . . . . . . . . . . . . . . . . . . . . . . . . . 100
17.4 Dot plot with multiple groups . . . . . . . . . . . . . . . . . . . . . . 101

18 Stripcharts 103
18.1 Basic stripcharts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
18.2 Add summary statistics . . . . . . . . . . . . . . . . . . . . . . . . . . 104
18.3 Change point shapes by groups . . . . . . . . . . . . . . . . . . . . . 105
18.4 Change colors by groups . . . . . . . . . . . . . . . . . . . . . . . . . 106
18.5 Stripchart with multiple groups . . . . . . . . . . . . . . . . . . . . . 108

19 Line Plots 110

19.1 Data format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
19.2 Basic line plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
19.3 Line plot with multiple groups . . . . . . . . . . . . . . . . . . . . . . 112
19.4 Line plot with a numeric x-axis . . . . . . . . . . . . . . . . . . . . . 113
19.5 Line plot with dates on x-axis: Time series . . . . . . . . . . . . . . . 115
CONTENTS 9

20 Bar Plots 118

20.1 Data format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
20.2 Basic bar plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
20.3 Change color by groups . . . . . . . . . . . . . . . . . . . . . . . . . . 120
20.4 Bar plot with multiple groups . . . . . . . . . . . . . . . . . . . . . . 121

21 Visualizing Error 124

21.1 Data format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
21.2 Compute mean and standard deviation . . . . . . . . . . . . . . . . . 124
21.3 Plot types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
21.4 Cross bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
21.5 Error bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
21.6 Horizontal error bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
21.7 Interval represented by a vertical line . . . . . . . . . . . . . . . . . . 132
21.8 Combine dot plot and error bars . . . . . . . . . . . . . . . . . . . . . 133

22 Pie Charts 135

22.1 Basic pie charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
22.2 Customized pie charts . . . . . . . . . . . . . . . . . . . . . . . . . . 136

V Graphical Parameters 138

23 Graphical Primitives 139

24 Main Titles, Axis Labels and Legend Title 142

24.1 Change the main title and axis labels . . . . . . . . . . . . . . . . . . 143
24.2 Change the appearance of labels . . . . . . . . . . . . . . . . . . . . . 143
24.3 Change legend titles . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
10 CONTENTS

25 Legend Position and Appearance 145

25.1 Change legend position and appearance . . . . . . . . . . . . . . . . . 145
25.2 guides() : set or remove the legend for a specific aesthetic . . . . . . . 147

26 Colors 150
26.1 Use a single color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
26.2 Change colors by groups . . . . . . . . . . . . . . . . . . . . . . . . . 151
26.3 Gradient or continuous colors . . . . . . . . . . . . . . . . . . . . . . 156

27 Point Shapes, colors and size 158

28 Line types 161

29 Axis limits: Minimum and Maximum values 164

30 Axis transformations: log and sqrt 166

31 Date Axes 170

31.1 Format axis tick mark labels: days, weeks, months . . . . . . . . . . . 170
31.2 Date axis limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172

32 Axis Ticks : Customize Tick Marks and Labels 173

33 Themes and Background Colors 178

33.1 Change plot themes: Quick functions . . . . . . . . . . . . . . . . . . 178
33.2 Customize plot background . . . . . . . . . . . . . . . . . . . . . . . 181
33.3 Use ggthemes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
33.4 Create your theme . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184

34 Text Annotations 185

34.1 Text annotations using geom_text and geom_label . . . . . . . . . . 186
34.2 annotation_custom : Add a static text annotation . . . . . . . . . . . 187
34.3 ggrepel: Avoid overlapping of text labels . . . . . . . . . . . . . . . . 188
CONTENTS 11

35 Add Straight Lines to a Plot 191

36 Rotate a Plot: Flip and Reverse 193

37 Facets: Split a Plot into a Matrix of Panels 194

38 Position Adjustements 199

39 Coordinate Systems 201

VI Extensions to ggplot2 203

40 Arrange Multiple Graphs on the Same Page 204

40.1 Required R packages . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
40.2 Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
40.3 cowplot: Arrange publication-ready plots . . . . . . . . . . . . . . . . 205
40.4 gridExtra package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
40.5 ggExtra: Add marginal distributions plots . . . . . . . . . . . . . . . 221
40.6 Insert an external graphical element inside a ggplot . . . . . . . . . . 222
40.7 Mix table, text and ggplot2 graphs . . . . . . . . . . . . . . . . . . . 225

41 Correlation Matrix Visualization 227

41.1 GGally . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
41.2 ggcorrplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229

42 Plotting Survival Curves 232

42.1 Fitting survival curves . . . . . . . . . . . . . . . . . . . . . . . . . . 232
42.2 Drawing survival curves with survminer . . . . . . . . . . . . . . . . . 233
12 CONTENTS

43 References and further reading 236

43.1 Extensions to ggplot2: R packages and functions . . . . . . . . . . . . 236
43.2 Cheat Sheets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
43.3 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
0.5. HOW THIS BOOK IS ORGANIZED? 13

0.5 How this book is organized?

This book contains 6 parts. The first part provides a quick introduction to R
(chapter 1) and to ggplot2 plotting system (chapter 2).
In the second part (chapter 3 - 11), we described the different graphs for visualiz-
ing one continous/discrete variable: area plots, density plots, histogram plots,
frequency polygon, dot plots, ECDF and QQ plots.
Density plot Histogram
0.08
30
0.06 sex sex
Density

count
F 20 F
0.04
M M
0.02 10

0.00 0

40 50 60 70 80 40 50 60 70 80
Weight weight
Empirical Cumulative QQ-Plot
Density Function 35
Miles/(US) gallon

1.00
30
cyl
0.75
F(weight)

25 4
0.50 20 6

0.25 8
15
0.00 10

52 54 56 58 60 -1 0 1
Weight theoretical
Part III provides quick-start guides for plotting two continuous/discretes vari-
ables, including :

Scatter plots (chapter 12)

Continuous bivariate distribution (chapter 13)
Jitter plots of two discretes variables (chapter 14)
14 CONTENTS

Scatter plot Scatter plot with 2d density

35
Miles/(US) gallon

30 90
cyl
80

waiting
25 4
70
20 6
60
15 8
50
10

2 3 4 5 2 3 4 5
Weight (lb/1000) eruptions
Part IV (chapter 15 - 22 ) describes how to draw and customize: box plots, violin
plots, dot plots, strip charts, line plots, bar plots and pie charts.
Box plot Strip chart

30 30
dose dose
Length

Length

0.5 0.5
20 20
1 1
2 2
10 10

0.5 1 2 0.5 1 2
Dose (mg) Dose (mg)
Dot plot Violin plot

30 30
dose dose
Length

Length

0.5 0.5
20 20
1 1
2 2
10 10

0.5 1 2 0.5 1 2
Dose (mg) Dose (mg)
0.5. HOW THIS BOOK IS ORGANIZED? 15

Bar plot Line plot

60 33 30

40 supp supp
20
len

len
OJ OJ
29.5 VC VC
20 15
10
6.8 10
0 4.2

D0.5 D1 D2 D0.5 D1 D2
dose dose
Pie chart

25% group
Child
Female
50% 25%
Male

Part V of the book covers how to change graphical parameters including:

Main title, axis labels and legend titles (chapter 24)

Legend position and appearance (chapter 25)
Colors (chapter 26)
Point shapes, colors and size (chapter 27)
Line types (chapter 28)
Axis limits: minimum and maximum values (chapter 29)
Axis transformations: log and sqrt (chapter 30)
Date axes (chapter 31)
Axis ticks : customize tick marks and labels (chapter 32)
Themes and background colors (chapter 33)
Add text annotations to a graph (chapter 34)
Add straight lines to a plot: horizontal, vertical and regression lines (chapter 35)
Rotate a plot (chapter 36)
Facets: split a plot into a matrix of panels (chapter 37)
Position adjustements (chapter 38)
16 CONTENTS

Coordinate systems (chapter 39)

Part VI describes some extensions of ggplot2 including:

Arranging multiple graphs on the same page (chapter 40)

Correlation matrix visualization (chapter 41)
Plotting survival curves (chapter 42)

Survival curves and correlation matrix:

Survival curves

Strata + sex=1 + sex=2

1.00
++
Survival probability

++
0.75 ++++
+ ++++++
++
++ ++
0.50 ++ +
++ +++ Correlation matrix
+++ ++
0.25 + drat
p = 0.0013 Corr
++ + 1.0
++ ++ mpg
0.00
qsec 0.5
0 250 500 750 1000
0.0
Time wt
-0.5
Number at risk by time disp
-1.0
Strata

sex=1 138 62 20 7 2 hp
sex=2 90 53 21 3 0
0 250 500 750 1000
hp

qs t
ec
pg
at
w
s

Time
dr
di

m
0.6. BOOK WEBSITE 17

Mixing multiple plots on the same page:

A B
30 dose 30 dose
0.5 0.5
len

len
20 20
1 1
10 2 10 2

0.5 1 2 0.5 1 2
dose dose
C
15
psavert

10
5

19701980199020002010
date
Each chapter is organized as an independent quick start guide. This means that,
you dont need to read the different chapters in sequence. I just recommend to read
firstly the chapter 1, as it gives a quick overview of R and ggplot2 graphing system.

For each chapter, the covered ggplot2 key functions are generally mentioned at the
beginning. The used data are described and many examples of R codes and graphics
are provided.
Sometimes, different chapters use the same data. In this case, we decided to repeat
the data preparation description in the corresponding chapters. In other words, each
chapter is an independent module and this gives the possibility to the user to read
only the chapter of interest.

0.6 Book website

The website for this book is located at : http://www.sthda.com/english/wiki/
ggplot2-essentials. It contains number of ressources.
18 CONTENTS

0.7 How to execute the R codes provided in this

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

Basics of R and ggplot2

19
Chapter 1

Introduction to R

R is a free and powerful statistical software for analyzing and visualizing data. If
you want to learn easily the essential of R programming, visit our series of tutorials
available on STHDA: http://www.sthda.com/english/wiki/r-basics-quick-and-easy.
In this chapter, we provide a very brief introduction to R, for installing R/RStudio as
well as importing your data into R.

1.1 Install R and RStudio

R and RStudio can be installed on Windows, MAC OSX and Linux platforms. RStudio
is an integrated development environment for R that makes using R easier. It includes
a console, code editor and tools for plotting.

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.

RStudio screen:

20
1.2. ARITHMETICS WITH R 21

1.2 Arithmetics with R

Basic arithmetic operations: + (addition), - (subtraction), * (multiplication),
/ (division), (exponentiation)

Type this in R console:

7 + 4 # => 11
7 - 4 # => 3
7 / 2 # => 3.5
7 * 2 # => 14

Basic arithmetic functions:

Logarithms and exponentials: log2(x), log10(x), exp(x)
Other mathematical functions: abs(x): absolute value; sqrt(x): square
root.

log2(4) # => 2
abs(-4) # => 4
sqrt(4) # => 2
22 CHAPTER 1. INTRODUCTION TO R

1.3 Data types in R

Basic data types: numeric, character and logical

my_age <- 28 # Numeric variable

my_name <- "Nicolas" # Character variable
# Are you a data scientist?: (yes/no) <=> (TRUE/FALSE)
is_datascientist <- TRUE # logical variable

Vectors: a combination of multiple values (numeric, character or logical)

Create a vector: c() for concatenate
Get a subset of a vector: my_vector[i] to get the ith element
Calculations with vectors: max(x), min(x), length(x), sum(x), mean(x),
sd(x): standard deviation, var(x): variance.

# Create a numeric vector

friend_ages <- c(27, 25, 29, 26)
mean(friend_ages) # => 26.75
max(friend_ages) # => 29
friend_ages[2] # age of my friends number 2 => 25

Matrices: like an Excel sheet containing multiple rows and columns. Combina-
tion of multiple vectors with the same types (numeric, character or logical).
Create and naming matrix: matrix(), cbind(), rbind(), rownames(x),
colnames(x)
Convert x to a matrix: x2 <- as.matrix(x)
Dimensions of a matrix: ncol(x), nrow(x), dim(x)
Get a subset of a matrix: my_data[row, col]
Calculations with numeric matrices: rowSums(x), colSums(x),
rowMeans(x), colMeans(x)

# Numeric vectors
col1 <- c(5, 6, 7, 8, 9)
col2 <- c(2, 4, 5, 9, 8)
1.3. DATA TYPES IN R 23

col3 <- c(7, 3, 4, 8, 7)

# Combine the vectors by column
my_data <- cbind(col1, col2, col3)
# Change rownames
rownames(my_data) <- c("row1", "row2", "row3", "row4", "row5")
my_data

## col1 col2 col3

## row1 5 2 7
## row2 6 4 3
## row3 7 5 4
## row4 8 9 8
## row5 9 8 7

Factors: grouping variables in your data

Create a factor: factor()
Convert x to a factor: x2 <- as.factor(x)
Calculations with factors:
Number of elements in each category: summary(x), table(x)
Compute some statistics by groups (for example, mean by groups):
tapply()

# Create a factor
friend_groups <- factor(c("grp1", "grp2", "grp1", "grp2"))
levels(friend_groups) # => "grp1", "grp2"

## [1] "grp1" "grp2"

# Compute the mean age by groups

friend_ages <- c(27, 25, 29, 26)
tapply(friend_ages, friend_groups, mean)

## grp1 grp2
## 28.0 25.5
24 CHAPTER 1. INTRODUCTION TO R

Data frames: like a matrix but can have columns with different types
Create a data frame: data.frame()
Convert x to a data frame: x2 <- as.data.frame(x)
Subset a data frame: my_data[row, col]

# Create a data frame

friends_data <- data.frame(
name = c("Nicolas", "Thierry", "Bernard", "Jerome"),
age = c(27, 25, 29, 26) ,
height = c(180, 170, 185, 169),
married = c(TRUE, FALSE, TRUE, TRUE)
)
friends_data

## name age height married

## 1 Nicolas 27 180 TRUE
## 2 Thierry 25 170 FALSE
## 3 Bernard 29 185 TRUE
## 4 Jerome 26 169 TRUE

Read more at: http://www.sthda.com/english/wiki/easy-r-programming-basics

1.4 Getting help with functions in R

If you want to learn more about a given function, say mean(), type this:

?mean

1.5 Installing and loading R packages

An R package is an extension of R containing data sets and specific R functions to

solve specific questions.
1.5. INSTALLING AND LOADING R PACKAGES 25

For example, in this book, youll learn how to draw beautiful graphs using the ggplot2
R package.
There are thousands other R packages available for download and installation from
CRAN, Bioconductor(biology related R packages) and GitHub repositories.

1. How to install packages from CRAN? Use the function install.packages():

# ggplot2: for data visualization

install.packages("ggplot2")

# dplyr: for data manipulation

install.packages("dplyr")

2. How to install packages from GitHub? You should first install devtools if you
dont have it already installed on your computer:

For example, the following R code installs the latest version of survminer R package
developed by A. Kassambara (https://github.com/kassambara/survminer).

install.packages("devtools")
devtools::install_github("kassambara/survminer")

Note that, GitHub contains the developmental version of R packages.

3. After installation, you must first load the package for using the functions in the
package. The function library() is used for this task.

library("ggplot2")

Now, we can use ggplot2 functions for drawing elegant graphs.

26 CHAPTER 1. INTRODUCTION TO R

1.6 Importing your data into R

1. Prepare your file as follow:

Use the first row as column names. Generally, columns represent variables
Use the first column as row names. Generally rows represent observations.
Each row/column name should be unique, so remove duplicated names.
Avoid names with blank spaces. Good column names: Long_jump or Long.jump.
Bad column name: Long jump.
Avoid names with special symbols: ?, $, *, +, #, (, ), -, /, }, {, |, >, < etc.
Only underscore can be used.
Avoid beginning variable names with a number. Use letter instead. Good column
names: sport_100m or x100m. Bad column name: 100m
R is case sensitive. This means that Name is different from Name or NAME.
Avoid blank rows in your data
Delete any comments in your file
Replace missing values by NA (for not available)
If you have a column containing date, use the four digit format. Good format:
01/01/2016. Bad format: 01/01/16

2. Our finale file should look like this:

3. Save your file

1.7. DEMO DATA SETS 27

We recommend to save your file into .txt (tab-delimited text file) or .csv (comma
separated value file) format.

4. Get your data into R:

Use the R code below. You will be asked to choose a file:

# .txt file: Read tab separated values

my_data <- read.delim(file.choose())

# .csv file: Read comma (",") separated values

my_data <- read.csv(file.choose())

# .csv file: Read semicolon (";") separated values

my_data <- read.csv2(file.choose())

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

1.7 Demo data sets

R comes with several built-in data sets, which are generally used as demo data for
playing with R functions.
The most used R demo data sets include: mtcars, iris, ToothGrowth and Plant-
Growth. To load a demo data set, use the function data() as follow:

# Loading
data(mtcars)

# Print the first 3 rows

head(mtcars, 3)
28 CHAPTER 1. INTRODUCTION TO R

## mpg cyl disp hp drat wt qsec vs am gear carb

## Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
## Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
## Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1

If you want learn more about mtcars data sets, type this:

?mtcars

mtcars data set is an object of class data frame.

To select just certain columns from a data frame, you can either refer to the columns
by name or by their location (i.e., column 1, 2, 3, etc.).

# Access the data in 'mpg' column

# dollar sign is used
mtcars$mpg

## [1] 21.0 21.0 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 17.8 16.4 17.3 15.2
## [15] 10.4 10.4 14.7 32.4 30.4 33.9 21.5 15.5 15.2 13.3 19.2 27.3 26.0 30.4
## [29] 15.8 19.7 15.0 21.4

# Or use this
mtcars[, 'mpg']

1.8 Close your R/RStudio session

Each time you close R/RStudio, you will be asked whether you want to save the data
from your R session. If you decide to save, the data will be available in future R
sessions.
Chapter 2

Introduction to ggplot2

2.1 Whats ggplot2?

ggplot2 is a powerful and a flexible R package, implemented by Hadley Wickham,
for producing elegant graphics. The gg in ggplot2 means Grammar of Graphics, a
graphic concept which describes plots by using a grammar.

According to ggplot2 concept, a plot can be divided into different fundamental parts
: Plot = data + Aesthetics + Geometry.

data: is a data frame

Aesthetics: is used to indicate x and y variables. It can be also used to control the
color, the size or the shape of points, the height of bars, etc.....

Geometry: corresponds to the type of graphics (histogram, box plot, line plot,
density plot, dot plot, ....)

Two main functions, for creating plots, are available in ggplot2 package :

qplot(): A quick plot function which is easy to use for simple plots.

ggplot(): A more flexible and robust function than qplot for building a plot piece
by piece.

29
30 CHAPTER 2. INTRODUCTION TO GGPLOT2

The output plot can be kept as a variable and then printed at any time using the
function print()
.
After creating plots, two other important functions are:

last_plot(): returns the last plot to be modified

ggsave("plot.png", width = 5, height = 5): saves the last plot in the current
working directory.

This document describes how to create and customize different types of graphs using
ggplot2. Many examples of code and graphics are provided.

2.2 Type of graphs for data visualization

The type of plots, to be created, depends on the format of your data. The ggplot2
package provides methods for visualizing the following data structures:

1. One variable - x: continuous or discrete

2. Two variables - x & y: continuous and/or discrete

3. Continuous bivariate distribution - x & y (both continuous)

4. Continuous function

5. Error bar

6. Maps

7. Three variables

In the current document well provide the essential ggplot2 functions for drawing
each of these seven data formats.
2.3. INSTALL AND LOAD GGPLOT2 PACKAGE 31

2.3 Install and load ggplot2 package

Use the R code below to install the latest version:

# Installation
install.packages('ggplot2')

# Loading
library(ggplot2)

2.4 Data format and preparation

The data must be a data.frame that contains all the information to make a ggplot.
In the data, columns should be variables and rows should be observations).

Well use the mtcars data set as an example of data:

# Load the data

data(mtcars)
df <- mtcars[, c("mpg", "cyl", "wt")]

# Convert cyl to a factor variable

df$cyl <- as.factor(df$cyl)

# Print a sample of the data

head(df)

## mpg cyl wt
## Mazda RX4 21.0 6 2.620
## Mazda RX4 Wag 21.0 6 2.875
## Datsun 710 22.8 4 2.320
## Hornet 4 Drive 21.4 6 3.215
## Hornet Sportabout 18.7 8 3.440
## Valiant 18.1 6 3.460
32 CHAPTER 2. INTRODUCTION TO GGPLOT2

2.5 qplot() function: Draw quick plots

The qplot() function is very similar to the standard R base plot() function. It can
be used to create quickly and easily different types of graphs: scatter plots, box
plots, violin plots, histogram and density plots.
A simplified format of qplot() is :

qplot(x, y = NULL, data, geom="auto")

x, y : x and y values, respectively. The argument y is optional depending on

the type of graphs to be created.

data : data frame to use (optional).

geom : Character vector specifying geom to use. Defaults to "point" if x and y

are specified, and "histogram" if only x is specified.

Other arguments such as main, xlab and ylab can be also used to add main title and
axis labels to the plot.

2.5.1 Scatter plots

The R code below creates basic scatter plots using the argument geom = point.
Its also possible to combine different geoms (e.g.: geom = c(point, smooth),
or geom = c(point, text)).

# Load data
data(mtcars)
# Basic scatter plot
qplot(x = mpg, y = wt, data = mtcars, geom = "point")

# Scatter plot with smoothed line

qplot(mpg, wt, data = mtcars,
geom = c("point", "smooth"))
2.5. QPLOT() FUNCTION: DRAW QUICK PLOTS 33

6
5
5
4 4
wt

wt
3 3

2
2
1
10 15 20 25 30 35 10 15 20 25 30 35
mpg mpg

The following R code will change the color and the shape of points by groups. The
column cyl will be used as grouping variable. In other words, the color and the shape
of points will be changed by the levels of cyl.

# Change the color by a continuous numeric variable

qplot(mpg, wt, data = mtcars, color = cyl)

# Change color and shape by groups (factor)

mtcars$cyl <- factor(mtcars$cyl)
qplot(mpg, wt, data = mtcars, colour = cyl, shape = cyl)

cyl
5 8 5
cyl
4 7 4 4
wt

wt

6 6
3 3
5 8
2 2
4
10 15 20 25 30 35 10 15 20 25 30 35
mpg mpg

Like color, the shape and the size of points can be controlled by a continuous or
discrete variable.

# Change the size of points according to

# the values of a continuous variable
qplot(mpg, wt, data = mtcars, size = mpg)
34 CHAPTER 2. INTRODUCTION TO GGPLOT2

2.5.2 Box plot, histogram and density plots

The R code below generates some data 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, 3)

## sex weight
## 1 F 53.79293
## 2 F 55.27743
## 3 F 56.08444

# Basic box plot from data frame

# Change fill color by sex
qplot(sex, weight, data = wdata,
geom = "boxplot")

# Basic histogram
qplot(weight, data = wdata, geom = "histogram")

# Density plot with main titles and axis labels

qplot(weight, data = wdata, geom = "density",
xlab = "Weight (kg)", ylab = "Density",
main = "Density plot")

30 Density plot
60 0.20
58
weight

count

20 0.15
Density

56 0.10
10
54 0.05

52 0 0.00
F M 52 54 56 58 60 52 54 56 58 60
sex weight Weight (kg)
2.6. GGPLOT() FUNCTION: BUILD PLOTS PIECE BY PIECE 35

2.6 ggplot() function: Build plots piece by piece

As mentioned above, the function ggplot() is powerful and more flexible than qplot().
This section describes briefly how to use ggplot() to build piece by piece an elegant
plot.
Recall that, the concept of ggplot divides a plot into three different fundamental
parts: plot = data + Aesthetics + geometry.
To demonstrate how the function ggplot() works, well draw a scatter plot. The
function aes() is used to specify x and y variables as well as aesthetics (e.g., color,
shape, size). An alternative option is the function aes_string() which, generates
mappings from a string.

# Basic scatter plot

ggplot(data = mtcars, aes(x = wt, y = mpg)) +
geom_point()

# Change the point size, and shape

ggplot(mtcars, aes(x = wt, y = mpg)) +
geom_point(size = 1.5, shape = 18)

35 35

30 30

25 25
mpg

mpg

20 20

15 15

10 10
2 3 4 5 2 3 4 5
wt wt
The function aes_string() can be used as follow:

ggplot(mtcars, aes_string(x = "wt", y = "mpg")) +

geom_point(size = 2, shape = 23)

Note that, some plots visualize a transformation of the original data set. In this
case, an alternative way to build a layer is to use stat_*() functions.
36 CHAPTER 2. INTRODUCTION TO GGPLOT2

In the following example, the function geom_density() does the same as the function
stat_density():

# Use geometry function

ggplot(wdata, aes(x = weight)) + geom_density()

# OR use stat function

ggplot(wdata, aes(x = weight)) + stat_density()

0.20 0.20

0.15 0.15
density

density

0.10 0.10

0.05 0.05

0.00 0.00
52 54 56 58 60 52 54 56 58 60
weight weight

For each plot type, well provide the geom_*() function and the corresponding
stat_*() function (if available).

In ggplot2 terminology, the functions geom_point() and geom_density() are

called layers. You can combine multiple layers as follow:

ggplot(data = mtcars, aes(x = wt, y = mpg)) +

geom_point() + # to draw points
geom_line() # to draw a line

35

30

25
mpg

20

15

10
2 3 4 5
wt
2.6. GGPLOT() FUNCTION: BUILD PLOTS PIECE BY PIECE 37

In the R code above, the two layers, geom_point() and geom_line(), use the same
data and the same aesthetic mapping provided in the main function ggplot.

Note that, its possible to use different data and mapping for different layers.

For example in the R code below:

The entire mtcars data is used by the layer geom_point()

A subset of mtcars data is used by the layer geom_line(). The line is colored
according to the values of the continuous variable cyl.

ggplot(data = mtcars, aes(x = wt, y = mpg)) +

geom_point() + # to draw points
geom_line(data = head(mtcars), color = "red")

35

30

25
mpg

20

15

10
2 3 4 5
wt

Its also possible to do simple calculations in the function aes().

# Log2 transformation in the aes()

ggplot(data = mtcars, aes(x = log2(wt), y = log2(mpg))) +
geom_point()
38 CHAPTER 2. INTRODUCTION TO GGPLOT2

log2(mpg) 5.0

4.5

4.0

3.5

1.0 1.5 2.0 2.5

log2(wt)

As mentioned above, the function aes_string() is used for aesthetic mappings from
string objects. An example is shown below:

ggplot(data = mtcars, aes_string(x = "wt", y = "mpg")) +

geom_point(color = "red") +
geom_smooth()

Note that, aes_string() is particularly useful when writing functions that create
plots because you can use strings to define the aesthetic mappings, rather than
having to use substitute to generate a call to aes() (see the R function below).

# Helper function for creating a scatter plot

# +++++++++++++++++++++
# data: data frame
# xName,yName: specify x and y variables, respectively
ggpoints <- function (data, xName, yName){
p <- ggplot(data = data, aes_string(xName, yName)) +
geom_point(color = "red") +
geom_smooth()

return(p)
}

Create a scatter plot using the helper function ggpoints():

ggpoints(mtcars, xName ="wt", yName = "mpg")

2.7. SAVE GGPLOTS 39

30
mpg

20

10
2 3 4 5
wt

2.7 Save ggplots

To print directly a ggplot to a file, the function print() is used:

# Print the plot to a pdf file

pdf("myplot.pdf")
myplot <- ggplot(mtcars, aes(wt, mpg)) + geom_point()
print(myplot)
dev.off()

For printing to a png file, use:

png("myplot.png")
print(myplot)
dev.off()

Its also possible to make a ggplot and to save it from the screen using the function
ggsave():

# 1. Create a plot: displayed on the screen (by default)

ggplot(mtcars, aes(wt, mpg)) + geom_point()
# 2.1. Save the plot to a pdf
ggsave("myplot.pdf")
# 2.2 OR save it to png file
ggsave("myplot.png")
 Part II

Plot One Variable - X: Continuous

or Discrete

40
2.8. DATA FORMAT 41

2.8 Data format

The R code below generates 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)

## sex weight
## 1 F 53.79293
## 2 F 55.27743
## 3 F 56.08444
## 4 F 52.65430

The following R code computes the mean value by sex, using dplyr package. First,
the data is grouped by sex and then summarised by computing the mean weight by
groups. The operator %>% is used to combine multiple operations:

library("dplyr")
mu <- wdata %>%
group_by(sex) %>%
summarise(grp.mean = mean(weight))

head(mu)

## Source: local data frame [2 x 2]

##
## sex grp.mean
## (fctr) (dbl)
## 1 F 54.94224
## 2 M 58.07325

In the next sections, the data mu well be used for adding mean line on the plots.
42

2.9 Plot types

We start by creating a plot, named a, that well finish in the next section by adding a
layer.

a <- ggplot(wdata, aes(x = weight))

Possible layers are:

For one continuous variable:

geom_area() for area plot
geom_density() for density plot
geom_dotplot() for dot plot
geom_freqpoly() for frequency polygon
geom_histogram() for histogram plot
stat_ecdf() for empirical cumulative density function
stat_qq() for quantile - quantile plot
For one discrete variable:
geom_bar() for bar plot

a + geom_area() a + geom_density() a + geom_dotplot() a + geom_freqpoly()

weight weight weight weight

a + geom_histogram() a + stat_ecdf() x + stat_qq() x + geom_bar()

weight weight theoretical fl

Chapter 3

Area Plots

An area plot is the continuous analog of a stacked bar chart (see Chapter 20).

Key function: geom_area()

Alternative function: stat_bin()

Key arguments to customize the plot: alpha, color, fill, linetype, size

# Basic plot
# Change line and fill colors
a + geom_area(stat = "bin",
color= "black", fill="#00AFBB")

30

20
count

10

0
52 54 56 58 60
weight

43
44 CHAPTER 3. AREA PLOTS

Note that, by default y axis corresponds to the count of weight values. If you want
to change the plot in order to have the density on y axis, the R code would be as
follow.

a + geom_area(aes(y = ..density..), stat ="bin")

The following plots compares bar plots and area plots. The diamonds data set [in
ggplot2 package] is used.

# Load the data

data("diamonds")
p <- ggplot(diamonds, aes(x = price, fill = cut))

# Bar plot
p + geom_bar(stat = "bin")

# Area plot
p + geom_area(stat = "bin")

cut cut
10000 Fair 10000 Fair
Good Good
count

count

Very Good Very Good

5000 5000
Premium Premium
Ideal Ideal

0 0
0 5000 100001500020000 0 5000 100001500020000
price price
Chapter 4

Density Plots

A kernel density estimate is useful for visualizing the distribution of a continuous

variable. The function geom_density() is used to create a density plot. You can
also add a line for the mean using the function geom_vline() [Chapter 35]

Key function: geom_density()

Alternative function: stat_density()

Key arguments to customize the plot: alpha, color, fill, linetype, size

4.1 Basic density plots

# Basic plot
a + geom_density()

# Change line color and fill color, add mean line

a + geom_density(color = "black", fill = "gray")+
geom_vline(aes(xintercept=mean(weight)),
color="#FC4E07", linetype="dashed", size=1)

45
46 CHAPTER 4. DENSITY PLOTS

0.20 0.20

0.15 0.15
density

density
0.10 0.10

0.05 0.05

0.00 0.00
52 54 56 58 60 52 54 56 58 60
weight weight

4.2 Change colors by groups

Density plot line and fill colors can be automatically controlled by the levels of sex:

# Change line colors by sex

a + geom_density(aes(color = sex))

# Change fill color by sex

# Use semi-transparent fill: alpha = 0.4
a + geom_density(aes(fill = sex), alpha=0.4)

# Add mean lines and color by sex

a + geom_density(aes(color = sex), alpha=0.4)+
geom_vline(data = mu, aes(xintercept = grp.mean, color=sex),
linetype="dashed")

0.4 0.4 0.4

0.3 sex 0.3 sex 0.3 sex

density

density

density

0.2 F 0.2 F 0.2 F

M M M
0.1 0.1 0.1

0.0 0.0 0.0

52 54 56 58 60 52 54 56 58 60 52 54 56 58 60
weight weight weight
4.2. CHANGE COLORS BY GROUPS 47

Change manually density plot line/fill colors using the functions :

scale_color_manual(), scale_fill_manual() : to use custom colors

scale_color_brewer(), scale_fill_brewer() : to use color palettes from RColor-
Brewer package
scale_color_grey(), scale_fill_grey() : to use grey color palettes

Change manually line colors:

# Add mean line and color manually

a2 <- a + geom_density(aes(color = sex)) +
geom_vline(data = mu, aes(xintercept = grp.mean, color = sex),
linetype="dashed") + theme_minimal()
a2 + scale_color_manual(values=c("#999999", "#E69F00"))

# Use brewer color palettes

a2 + scale_color_brewer(palette="Paired")

# Use grey scale

a2 + scale_color_grey()

0.4 0.4 0.4

0.3 sex 0.3 sex 0.3 sex

density

density

density

0.2 F 0.2 F 0.2 F

M M M
0.1 0.1 0.1

0.0 0.0 0.0

5254565860 5254565860 5254565860

weight weight weight
48 CHAPTER 4. DENSITY PLOTS

Change manually fill colors:

# Fill manually
a3 <- a + geom_density(aes(fill = sex), alpha = 0.4) + theme_minimal()
a3 + scale_fill_manual(values=c("#999999", "#E69F00"))

# Use brewer color palettes

a3 + scale_fill_brewer(palette="Dark2") + theme_minimal()

# Use grey scale

a3 + scale_fill_grey() + theme_minimal()

0.4 0.4 0.4

0.3 sex 0.3 sex 0.3 sex

density

density

density
0.2 F 0.2 F 0.2 F
M M M
0.1 0.1 0.1

0.0 0.0 0.0

5254565860 5254565860 5254565860

weight weight weight
Read more on ggplot2 colors here: Chapter 26
Chapter 5

Histogram Plots

A Histogram represents the distribution of a continuous variable by dividing

into bins and counting the number of observations in each bin. The function
geom_histogram() is used to create a histogram plot. You can also add a line
for the mean using the function geom_vline() [Chapter 35].

Key function: geom_histogram()

Alternative functions: stat_bin()

Position adjustments: "identity" (or position_identity()), "stack" (or posi-

tion_stack()), "dodge" ( or position_dodge()). Default value is "stack"

Key arguments to customize the plot: alpha, color, fill, linetype, size

49
50 CHAPTER 5. HISTOGRAM PLOTS

5.1 Basic histogram plots

# Basic plot
a + geom_histogram()

# Change the number of bins

a + geom_histogram(bins = 50)

# Change line color and fill color, add mean line

a + geom_histogram(color = "black", fill = "gray")+
geom_vline(aes(xintercept=mean(weight)),
color="#FC4E07", linetype="dashed", size=1)

30 20 30

15
20 20
count

count

10 count
10 10
5

0 0 0
52 54 56 58 60 52 54 56 58 60 52 54 56 58 60
weight weight weight

Note that by default, stat_bin uses 30 bins - this might not be good default. You
can change the number of bins (e.g.: bins = 50 or the bin width e.g.: binwidth
= 0.5.

By default y axis corresponds to the count of weight values. If you want to change
the plot in order to have the density on y axis, the R code would be as follow.

a + geom_histogram(aes(y = ..density..))
5.2. CHANGE COLORS BY GROUPS 51

5.2 Change colors by groups

Histogram plot line colors can be automatically controlled by the levels of the variable
sex.

You can change the position adjustment to use for overlapping points on the layer.
Possible values for the argument position are "identity", "stack", "dodge". Default
value is "stack".

# Change line colors by sex

a + geom_histogram(aes(color = sex), fill = "white")

# Position adjustment: "identity" (overlaid)

a + geom_histogram(aes(color = sex), fill = "white", alpha = 0.6,
position="identity")

# Position adjustment: "dodge" (Interleaved)

# Add mean lines and color by sex
a + geom_histogram(aes(color = sex), fill = "white",
position="dodge") +
geom_vline(data = mu, aes(xintercept = grp.mean, color=sex),
linetype="dashed")

30 30

20 sex 20 sex
count

count

F F
M M
10 10

0 0
52 54 56 58 60 52 54 56 58 60
weight weight
52 CHAPTER 5. HISTOGRAM PLOTS

30

20 sex
count

F
M
10

0
52 54 56 58 60
weight

As described in the density plot chapter (Chapter 4), line and fill colors can be changed
manually as follow:

# Use classic theme and change legend position to "top"

# Change outline color manually
a + geom_histogram(aes(color = sex), fill = "white",
alpha = 0.4, position = "identity") +
scale_color_manual(values=c("#00AFBB", "#E7B800"))

# change fill and outline color manually

a + geom_histogram(aes(color = sex, fill = sex),
alpha = 0.4, position = "identity") +
scale_fill_manual(values=c("#00AFBB", "#E7B800")) +
scale_color_manual(values=c("#00AFBB", "#E7B800"))

30 30

20 sex 20 sex
count

count

F F
M M
10 10

0 0
52 54 56 58 60 52 54 56 58 60
weight weight

Read more on ggplot2 colors here: Chapter 26

Chapter 6

Combine Histogram and Density

Plots

Plot histogram with density values on y-axis (instead of count values).

Add density plot with transparent density plot

# Histogram with density plot

a + geom_histogram(aes(y=..density..), colour="black", fill="white") +
geom_density(alpha=0.2, fill = "#FF6666")

# Color by groups
a + geom_histogram(aes(y=..density.., color = sex, fill = sex),
alpha=0.5, position="identity")+
geom_density(aes(color = sex), size = 1)

0.2 0.4
sex
density

density

F
0.1 0.2 M

0.0 0.0
52 54 56 58 60 52 54 56 58 60
weight weight

53
Chapter 7

Frequency Polygon

Frequency polygon is very close to histogram plots (Chapter: 5). It can be also used to
visualize the distribution of a continuous variable. The difference between histograms
and frequency polygon is that:

Histograms use bars

Frequency polygons use lines.

The function geom_freqpoly() is used to create a frequency polygon.

Key function: geom_freqpoly()

Alternative functions: stat_bin()

Key arguments to customize the plot: alpha, color, linetype, size

54
 55

# Basic plot
a + geom_freqpoly(bins = 30) +
theme_minimal()

# Change color and linetype by sex

# Use custom color palettes
a + geom_freqpoly(aes(color = sex, linetype = sex))+
scale_color_manual(values=c("#999999", "#E69F00"))+
theme_minimal()

30 30
sex
count

20 count 20
F
10 10 M

0 0

52 54 56 58 60 52 54 56 58 60
weight weight

If you want to change the plot in order to have the density on y axis, the R code
would be as follow.

a + geom_freqpoly(aes(y = ..density..))
Chapter 8

Dot Plots for One Variable

In a dot plot, dots are stacked with each dot representing one observation. The
width of a dot corresponds to the bin width.

Key function: geom_dotplot()

Key arguments to customize the plot: alpha, color, fill and dotsize

# change fill and color by sex

a + geom_dotplot(aes(fill = sex))

1.00

0.75
sex
count

0.50 F
M
0.25

0.00
52 54 56 58 60
weight

56
Chapter 9

ECDF Plots

ECDF (Empirical Cumulative Density Function) reports for any given number the
percent of individuals that are below that threshold.

Key function: stat_ecdf()

Key arguments to customize the plot: alpha, color, linetype and size

a + stat_ecdf(geom = "point")
a + stat_ecdf(geom = "step")

1.00 1.00
0.75 0.75
0.50 0.50
y

0.25 0.25
0.00 0.00
52 54 56 58 60 52 54 56 58 60
weight weight

For any value, say, height = 50, you can see that about 25% of our individuals are
shorter than 50 inches.

57
Chapter 10

QQ Plots

QQ-plots (or Quantile - Quantile plots) are used to check whether a given data
follows normal distribution. The function stat_qq() or qplot() can be used to create
qq-plots.

Key function: stat_qq()

Key arguments to customize the plot: alpha, color, shape and size

mtcars data sets are used in the examples below.

data(mtcars)
# Convert cyl column from a numeric to a factor variable
mtcars$cyl <- as.factor(mtcars$cyl)
head(mtcars[, c("mpg", "cyl")])

## mpg cyl
## Mazda RX4 21.0 6
## Mazda RX4 Wag 21.0 6
## Datsun 710 22.8 4
## Hornet 4 Drive 21.4 6
## Hornet Sportabout 18.7 8
## Valiant 18.1 6

58
 59

Create qq plots

p <- ggplot(mtcars, aes(sample=mpg))

# Basic plot
p + stat_qq()

# Change point shapes by groups

# Use custom color palettes
p + stat_qq(aes(shape = cyl, color = cyl))+
scale_color_manual(values=c("#00AFBB", "#E7B800", "#FC4E07"))

35 35

30 30
cyl
sample

sample

25 25 4

20 20 6
8
15 15

10 10
-2 -1 0 1 2 -1 0 1
theoretical theoretical
Read more on ggplot2 colors here: Chapter 26
Chapter 11

Bar Plots of Counts

The function geom_bar() can be used to visualize one discrete variable. In this case,
the count of each level is plotted.

Key function: geom_bar()

Alternative function: stat_count()

Key arguments to customize the plot: alpha, color, fill, linetype and size

Well use the mpg data set [in ggplot2 package]. The R code is as follow:

data(mpg)
ggplot(mpg, aes(fl)) +
geom_bar(fill = "steelblue")+ theme_minimal()

150
count

100
50
0

c d e p r
fl

60
 Part III

Plot Two Variables - X & Y: Both

Continuous or Discrete

61
Chapter 12

Scatter plots: Continuous X and Y

12.1 Data format

Well use the mtcars data set. The variable cyl is used as grouping variable.

data(mtcars)
mtcars$cyl <- as.factor(mtcars$cyl)
head(mtcars[, c("wt", "mpg", "cyl")], 3)

## wt mpg cyl
## Mazda RX4 2.620 21.0 6
## Mazda RX4 Wag 2.875 21.0 6
## Datsun 710 2.320 22.8 4

12.2 Plot types

We start by creating a plot, named b, that well finish in the next section by adding a
layer.

b <- ggplot(mtcars, aes(x = wt, y = mpg))

Possible layers include:

62
12.3. BASIC SCATTER PLOTS 63

geom_point() for scatter plot

geom_smooth() for adding smoothed line such as regression line
geom_quantile() for adding quantile lines
geom_rug() for adding a marginal rug
geom_jitter() for avoiding overplotting
geom_text() for adding textual annotations

b + geom_point() b + geom_smooth() b + geom_quantile() b + geom_rug()

wt wt wt wt
b + geom_jitter() b + geom_text()
Toyota Corolla
Fiat 128
Honda Civic

Hornet
Mazda 4 Drive
RX4
Ferrari Dino
Pontiac
ValiantFirebird
Merc 450SE

Lincoln Continental
wt wt

12.3 Basic scatter plots

The function geom_point() is used to create a scatter plot.

Key function: geom_point()

Key arguments to customize the plot: alpha, color, fill, shape and size

The color, the size and the shape of points can be changed using the function
geom_point() as follow :
64 CHAPTER 12. SCATTER PLOTS: CONTINUOUS X AND Y

geom_point(size, color, shape)

Note that, the size of the points can be also controlled by the values of a continuous
variable.

# Basic scatter plot

b + geom_point(color = "#00AFBB")

# Change the point size, and shape

b + geom_point(color = "#00AFBB", size = 2, shape = 23)

35 35

30 30

25 25
mpg

mpg

20 20

15 15

10 10
2 3 4 5 2 3 4 5
wt wt

# Control point size by continuous variable values

b + geom_point(aes(size=qsec), color = "#00AFBB")
12.4. SCATTER PLOTS WITH MULTIPLE GROUPS 65

35

30

qsec
25 15.0
mpg

17.5
20 20.0
22.5
15

10
2 3 4 5
wt
Read more on point shapes: Chapter 27
Its possible to use the function geom_text() for adding point labels:

b + geom_point() +
geom_text(label=rownames(mtcars), nudge_x = 0.5)

Read more on text annotations : Chapter 34

12.4 Scatter plots with multiple groups

This section describes how to change point colors and shapes automatically and
manually.

1. Change the point color/shape/size automatically: In the R code below,

point shapes, colors and sizes are controlled automatically by the levels of the
grouping variable cyl :

# Change point shapes by the levels of cyl

b + geom_point(aes(shape = cyl))

# Change point shapes and colors

b + geom_point(aes(shape = cyl, color = cyl))
66 CHAPTER 12. SCATTER PLOTS: CONTINUOUS X AND Y

35 35

30 30
cyl cyl
25 4 25 4
mpg

mpg
20 6 20 6
8 8
15 15

10 10
2 3 4 5 2 3 4 5
wt wt
12.4. SCATTER PLOTS WITH MULTIPLE GROUPS 67

2. Change the point color/shape/size manually

The functions below are used :

scale_shape_manual() for point shapes

scale_color_manual() for point colors
scale_size_manual() for point sizes

# Change the point sizes manually

b + geom_point(aes(color = cyl, shape = cyl, size = cyl)) +
scale_size_manual(values=c(2,3,4))

# Change point shapes and colors manually

b + geom_point(aes(color = cyl, shape = cyl)) +
scale_shape_manual(values=c(3, 16, 17))+
scale_color_manual(values=c('#999999','#E69F00', '#56B4E9'))

35 35

30 30
cyl cyl
25 25
4 4
mpg

mpg

6 6
20 20
8 8
15 15

10 10
2 3 4 5 2 3 4 5
wt wt
68 CHAPTER 12. SCATTER PLOTS: CONTINUOUS X AND Y

scale_color_brewer() : to use color palettes from RColorBrewer package

scale_color_grey() : to use grey color palettes

# use brewer color palettes

b + geom_point(aes(color = cyl, shape = cyl)) +
scale_color_brewer(palette="Dark2") + theme_minimal()

# Use grey scale

b + geom_point(aes(color = cyl, shape = cyl)) +
scale_color_grey()+ theme_minimal()

35 35

30 30
cyl cyl
25 4 25 4
mpg

mpg

20 6 20 6
8 8
15 15

10 10

2 3 4 5 2 3 4 5
wt wt
Read more on ggplot2 colors here : Chapter 26

12.5 Add regression line or smoothed conditional

mean

Key functions: geom_smooth() and geom_abline() (Chapter 35)

Alternative functions: stat_smooth()

Key arguments to customize the plot: alpha, color, fill, shape, linetype
and size
12.5. ADD REGRESSION LINE OR SMOOTHED CONDITIONAL MEAN 69

Only the function geom_smooth() is covered in this section.

A simplified format is :

geom_smooth(method="auto", se=TRUE, fullrange=FALSE, level=0.95)

method : smoothing method to be used. Possible values are lm, glm, gam,
loess, rlm.
method = loess: This is the default value for small number of obser-
vations. It computes a smooth local regression. You can read more about
loess using the R code ?loess.
method =lm: It fits a linear model. Note that, its also possible to
indicate the formula as formula = y ~ poly(x, 3) to specify a degree 3
polynomial.
se : logical value. If TRUE, confidence interval is displayed around smooth.
fullrange : logical value. If TRUE, the fit spans the full range of the plot
level : level of confidence interval to use. Default value is 0.95

To add a regression line on a scatter plot, the function geom_smooth() is used

in combination with the argument method = lm. lm stands for linear model.

# Add regression line

b + geom_point() + geom_smooth(method = lm)

# Point + regression line

# Remove the confidence interval
b + geom_point() +
geom_smooth(method = lm, se = FALSE)

# loess method: local regression fitting

b + geom_point() + geom_smooth()
70 CHAPTER 12. SCATTER PLOTS: CONTINUOUS X AND Y

35

30 30
30
25
mpg

mpg

mpg
20
20 20

15
10
10 10

2 3 4 5 2 3 4 5 2 3 4 5
wt wt wt
Change point color and shapes by groups:

# Change color and shape by groups (cyl)

b + geom_point(aes(color = cyl, shape=cyl)) +
geom_smooth(aes(color = cyl, fill = cyl), method = lm)

# Remove confidence intervals

# Extend the regression lines: fullrange
b + geom_point(aes(color = cyl, shape = cyl)) +
geom_smooth(aes(color = cyl), method = lm, se = FALSE,
fullrange = TRUE)

35
35

30
30
cyl cyl
25 25
4 4
mpg

mpg

6 20 6
20
8 8
15 15

10 10

2 3 4 5 2 3 4 5
wt wt
12.6. ADD QUANTILE LINES FROM A QUANTILE REGRESSION 71

12.6 Add quantile lines from a quantile regression

Quantile lines can be used as a continuous analogue of a geom_boxplot().

Key function: geom_quantile()

Alternative functions: stat_quantile()

Key arguments to customize the plot: alpha, color, linetype and size

Well use the mpg data set [in ggplot2].

The function geom_quantile() can be used for adding quantile lines:

ggplot(mpg, aes(cty, hwy)) +

geom_point() + geom_quantile() +
theme_minimal()

50

40
hwy

30

20

10

10 15 20 25 30 35
cty
72 CHAPTER 12. SCATTER PLOTS: CONTINUOUS X AND Y

12.7 Add marginal rugs to a scatter plot

Key function: geom_rug()

Key arguments to customize the plot: alpha, color and size

The function geom_rug() can be used as follow :

geom_rug(sides ="bl")

Sides : a string that controls which sides of the plot the rugs appear on. Allowed
value is a string containing any of trbl, for top, right, bottom, and left.

# Add marginal rugs

b + geom_point() + geom_rug()

# Change colors by groups

b + geom_point(aes(color = cyl)) +
geom_rug(aes(color = cyl))

# Add marginal rugs using faithful data

data(faithful)
ggplot(faithful, aes(x = eruptions, y = waiting)) +
geom_point() + geom_rug()

35 35
90
30 30
cyl
80
waiting

25 25 4
mpg

mpg

70
20 20 6
60
8
15 15 50
10 10
2 3 4 5 2 3 4 5 2 3 4 5
wt wt eruptions
12.8. JITTER POINTS TO REDUCE OVERPLOTTING 73

12.8 Jitter points to reduce overplotting

Key functions: geom_jitter() and position_jitter()

Key arguments to customize the plot: alpha, color, fill, shape and size

The function geom_jitter() is a convenient default for geom_point(position =

jitter). The mpg data set [in ggplot2] is used in the following examples.

p <- ggplot(mpg, aes(displ, hwy))

# Default scatter plot
p + geom_point()

# Use jitter to reduce overplotting

p + geom_jitter(position = position_jitter(width = 0.5, height = 0.5))

40 40

30 30
hwy

hwy

20 20

2 3 4 5 6 7 2 3 4 5 6 7
displ displ

To adjust the extent of jittering, the function position_jitter() with the arguments
width and height are used:

width: degree of jitter in x direction.

height: degree of jitter in y direction.
74 CHAPTER 12. SCATTER PLOTS: CONTINUOUS X AND Y

12.9 Textual annotations

Key function: geom_text()

Key arguments to customize the plot: label, alpha, angle, color, family,
fontface, hjust, lineheight, size, and vjust.

The argument label is used to specify a vector of labels for point annotations.

b + geom_text(aes(label = rownames(mtcars)),
size = 3)

35
Toyota Corolla
Fiat 128
Lotus
30Honda
Europa
Civic

Fiat X1-9
Porsche 914-2
25 Merc 240D
mpg

Datsun 710 Merc 230

Toyota Corona
Volvo
Mazda
Mazda 142EWag
Hornet
RX4
RX4 4 Drive
20 Ferrari Dino
Hornet Pontiac
Merc 280 Firebird
Sportabout
Valiant
Merc 280C
Merc 450SL
Ford Pantera Merc
L 450SE
15 Dodge
AMC Challenger
Javelin
Merc
Maserati 450SLC
Bora
Duster 360 Chrysler Imperial
Camaro Z28

10 Cadillac
LincolnFleetwood
Continental
2 3 4 5
wt
Chapter 13

Continuous bivariate distribution

13.1 Data format

Well use the diamonds data set [in ggplot2]:

data(diamonds)
head(diamonds[, c("carat", "price")])

## Source: local data frame [6 x 2]

##
## carat price
## (dbl) (int)
## 1 0.23 326
## 2 0.21 326
## 3 0.23 327
## 4 0.29 334
## 5 0.31 335
## 6 0.24 336

13.2 Plot types

We start by creating a plot, named c, that well finish in the next section by adding a
layer.

75
76 CHAPTER 13. CONTINUOUS BIVARIATE DISTRIBUTION

c <- ggplot(diamonds, aes(carat, price))

Possible layers include:

geom_bin2d() for adding a heatmap of 2d bin counts. Rectangular bining.

geom_hex() for adding hexagon bining. The R package hexbin is required
for this functionality
geom_density_2d() for adding contours from a 2d density estimate

c + geom_bin() c + geom_hex() c + geom_density_2d()

carat carat carat

13.3 Add heatmap of 2d bin counts

The function geom_bin2d() produces a scatter plot with rectangular bins. The
number of observations is counted in each bins and displayed as a heatmap.

Key function: geom_bin2d()

Alternative functions: stat_bin_2d(), stat_summary_2d()

Key arguments to customize the plot: max, xmin, ymax, ymin, alpha,
color, fill, linetype and size.

# Default plot
c + geom_bin2d()
13.4. ADD HEXAGON BINING 77

# Change the number of bins

c + geom_bin2d(bins = 15)

# Or specify the width of bins

c + geom_bin2d(binwidth=c(1, 1000))

20000 20000
count count
15000 15000
6000 7500
price

price
10000 10000
4000 5000

5000 2000 5000 2500

0 0
0 1 2 3 4 5 0 1 2 3 4 5
carat carat
count
15000

10000
price

10000

5000 5000

0
0 2 4 6
carat
Alternative functions:

c + stat_bin_2d()

c + stat_summary_2d(aes(z = depth))

13.4 Add hexagon bining

The function geom_hex() produces a scatter plot with hexagon bining. The hexbin
R package is required for hexagon bining. If you dont have it, use the R code below
78 CHAPTER 13. CONTINUOUS BIVARIATE DISTRIBUTION

to install it:

install.packages("hexbin")

Key function: geom_hex()

Alternative functions: stat_bin_hex(), stat_summary_hex()

Key arguments to customize the plot: alpha, color, fill and size.

The function geom_hex() can be used as follow:

require(hexbin)
# Default plot
c + geom_hex()

# Change the number of bins

c + geom_hex(bins = 10)

20000
value value
15000 5000 15000
7500
4000
price

price

10000 10000
3000 5000
5000 2000 5000
2500
1000
0 0
0 1 2 3 4 5 0 1 2 3 4 5
carat carat
Alternative functions:

c + stat_bin_hex()

c + stat_summary_hex(aes(z = depth))
13.5. SCATTER PLOTS WITH 2D DENSITY ESTIMATION 79

13.5 Scatter plots with 2d density estimation

The functions geom_density_2d() or stat_density_2d() can be used to add 2d
density estimate to a scatter plot.

Key function: geom_density_2d()

Alternative function: stat_density_2d()

Key arguments to customize the plot: alpha, color, linetype and size.

faithful data set is used in this section, and we first start by creating a scatter plot
(sp) as follow:

data("faithful")
# Scatter plot
sp <- ggplot(faithful, aes(x = eruptions, y = waiting))

# Default plot
sp + geom_density_2d(color = "#E7B800")
# Add points
sp + geom_point(color = "#00AFBB") +
geom_density_2d(color = "#E7B800")

90 90

80 80
waiting

waiting

70 70

60 60

50 50

2 3 4 5 2 3 4 5
eruptions eruptions
80 CHAPTER 13. CONTINUOUS BIVARIATE DISTRIBUTION

# Use stat_density_2d with geom = "polygon"

sp + geom_point() +
stat_density_2d(aes(fill = ..level..), geom="polygon")

# Change the gradient color

sp + geom_point() +
stat_density_2d(aes(fill = ..level..), geom="polygon") +
scale_fill_gradient(low="#00AFBB", high="#FC4E07")

level level
90 90

80 0.020 80 0.020
waiting

waiting
70 0.015 70 0.015

60 0.010 60 0.010

50 0.005 50 0.005

2 3 4 5 2 3 4 5
eruptions eruptions

Alternative function:

sp + stat_density_2d()

See also: ?stat_contour(), ?geom_contour()

13.6 Continuous function

In this section, well see how to connect observations by line.

Key functions: geom_area(), geom_line(), geom_step()

Key arguments to customize the plot: alpha, color, linetype, size and fill
(for geom_area only).
13.6. CONTINUOUS FUNCTION 81

The economics data set [in ggplot2] is used.

data(economics)
# head(economics)

We start by creating a plot, named d, that well finish by adding a layer.

d <- ggplot(economics, aes(x = date, y = unemploy))

Possible layers include:

geom_area() for area plot

geom_line() for line plot connecting observations, ordered by x
geom_step() for connecting observations by stairs

# Area plot
d + geom_area(fill = "#00AFBB", color = "white")

# Line plot: connecting observations, ordered by x

d + geom_line(color = "#E7B800")

# Connecting observations by stairs

# a subset of economics data set is used
set.seed(1234)
ss <- economics[sample(1:nrow(economics), 15), ]
ggplot(ss, aes(x = date, y = unemploy)) +
geom_step(color = "#FC4E07")

15000 15000
12500
unemploy

unemploy

unemploy

12000
10000 10000
8000 7500
5000
4000 5000
0 2500
19701980199020002010 19701980199020002010 1970 1980 1990 2000 2010
date date date
Chapter 14

Two variables: Discrete X,

Discrete Y

Key function: geom_jitter()

Key arguments to customize the plot: alpha, color, fill, shape and size.

The diamonds data set [in ggplot2] well be used to plot the discrete variable color
(for diamond colors) by the discrete variable cut (for diamond cut types). The plot is
created using the function geom_jitter().

data("diamonds")
ggplot(diamonds, aes(cut, color)) +
geom_jitter(aes(color = cut), size = 0.5)

82
 83

H cut
Fair
Good
color

G
Very Good
Premium

F Ideal

Fair Good Very Good Premium Ideal

cut
 Part IV

Plot Two Variables - X & Y:

Discrete X and Continuous Y

84
14.1. DATA FORMAT 85

14.1 Data format

The ToothGrowth data set well be used to plot the continuous variable len (for
tooth length) by the discrete variable dose. The following R code converts the variable
dose from a numeric to a discrete factor variable.

data("ToothGrowth")
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
head(ToothGrowth)

## 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

14.2 Plot types

We start by creating a plot, named e, that well finish in the next section by adding a
layer.

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

Possible layers include:

geom_boxplot() for box plot

geom_violin() for violin plot
geom_dotplot() for dot plot
geom_jitter() for stripchart
geom_line() for line plot
geom_bar() for bar plot
86

e + geom_boxplot() e + geom_violin() e + geom_dotplot() e + geom_jitter()

dose dose dose dose

e + geom_line() e + geom_bar()

dose dose
Chapter 15

Box Plots

Box plots display a group of numerical data through their quartiles.

Key function: geom_boxplot()

Alternative function: stat_boxplot()

Key arguments to customize the plot: alpha, color, linetype, shape, size
and fill.

The function geom_boxplot() is used to create a box plot. 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, makes 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.

87
88 CHAPTER 15. BOX PLOTS

15.1 Basic box plots

# Basic box plot

e + geom_boxplot()

# Rotate the box plot

e + geom_boxplot() + coord_flip()

# Notched box plot

e + geom_boxplot(notch = TRUE)

# Box plot with mean points

e + geom_boxplot() +
stat_summary(fun.y = mean, geom = "point",
shape = 18, size = 4, color = "blue")

30 2 30 30
dose
len

len

len
20 1 20 20

10 0.5 10 10

0.5 1 2 10 20 30 0.5 1 2 0.5 1 2

dose len dose dose

Its possible to use the function scale_x_discrete() for:

choosing which items to display: for example c("0.5", "2"),

changing the order of items: for example from c("0.5", "1", "2") to c("2", "0.5",
"1")

# Choose which items to display: group "0.5" and "2"

e + geom_boxplot() +
scale_x_discrete(limits=c("0.5", "2"))

# Change the default order of items

15.2. CHANGE COLORS BY GROUPS 89

e + geom_boxplot() +
scale_x_discrete(limits=c("2", "0.5", "1"))

30 30
len

len
20 20

10 10

0.5 2 2 0.5 1
dose dose

Alternative functions: stat_boxplot()

e + stat_boxplot(coeff = 1.5)

15.2 Change colors by groups

Box plot outline and fill colors can be automatically controlled by the levels of the
grouping variable dose:

# Use single colors

e + geom_boxplot(color = "black", fill = "steelblue")

# Change outline colors by dose (groups)

e + geom_boxplot(aes(color = dose))

# Change fill color by dose (groups)

e + geom_boxplot(aes(fill = dose))
90 CHAPTER 15. BOX PLOTS

30 30 30
dose dose
0.5 0.5
len

len

len
20 20 20
1 1
2 2
10 10 10

0.5 1 2 0.5 1 2 0.5 1 2

dose dose dose
Change manually box plot outline/fill colors using the functions :

scale_color_manual(), scale_fill_manual() : to use custom colors

scale_color_brewer(), scale_fill_brewer() : to use color palettes from RColor-
Brewer package
scale_color_grey(), scale_fill_grey() : to use grey color palettes

Change manually outline colors:

# Use custom color palettes

e2 <- e + geom_boxplot(aes(color = dose)) + theme_minimal()
e2 + scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))

# Use brewer color palettes

e2 + scale_color_brewer(palette="Dark2")

# Use grey scale

e2 + scale_color_grey()

30 dose 30 dose 30 dose

0.5 0.5 0.5
len

len

len

20 20 20
1 1 1
10 2 10 2 10 2

0.5 1 2 0.5 1 2 0.5 1 2

dose dose dose
15.3. BOX PLOT WITH MULTIPLE GROUPS 91

Change manually fill colors:

# Use custom color palettes

e3 <- e + geom_boxplot(aes(fill = dose)) + theme_minimal()
e3 + scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))

# Use brewer color palettes

e3 + scale_fill_brewer(palette="Dark2")

# Use grey scale

e3 + scale_fill_grey()

30 dose 30 dose 30 dose

0.5 0.5 0.5
len

len

len
20 20 20
1 1 1
10 2 10 2 10 2

0.5 1 2 0.5 1 2 0.5 1 2

dose dose dose
Read more on ggplot2 colors here: Chapter 26

15.3 Box plot with multiple groups

The grouping variables dose and supp are used:

# Change box plot colors by groups

e + geom_boxplot(aes(fill = supp))

# Change the position

e + geom_boxplot(aes(fill = supp), position = position_dodge(1))

# Change fill colors

e + geom_boxplot(aes(fill = supp), position = position_dodge(1)) +
scale_fill_manual(values=c("#999999", "#E69F00"))
92 CHAPTER 15. BOX PLOTS

30 30

supp supp
20 20
len

len
OJ OJ
VC VC

10 10

0.5 1 2 0.5 1 2
dose dose

30

supp
20
len

OJ
VC

10

0.5 1 2
dose
Chapter 16

Violin plots

Violin plots are similar to box plots (Chapter 15), except that they also show the
kernel probability density of the data at different values. Typically, violin plots will
include a marker for the median of the data and a box indicating the interquartile
range, as in standard box plots.
The function geom_violin() is used to produce a violin plot.

Key function: geom_violin()

Alternative function: stat_ydensity()

Key arguments to customize the plot: alpha, color, linetype, size and fill.

16.1 Basic violin plots

# Basic box plot

e + geom_violin()
# Rotate the violin plot
e + geom_violin() + coord_flip()
# Set trim argument to FALSE
e + geom_violin(trim = FALSE, fill = "steelblue")

93
94 CHAPTER 16. VIOLIN PLOTS

30 2 30

dose
len

len
20 1 20

10 0.5 10

0.5 1 2 10 20 30 0.5 1 2
dose len dose

Note that by default trim = TRUE. In this case, the tails of the violins are trimmed.
If FALSE, the tails are not trimmed.

To change the order of items (or to select some of the items), the function
scale_x_discrete() can be used as described in Chapter 15.

16.2 Add summary statistics

The function stat_summary() can be used to add mean/median points and more
on a violin plot

# Add mean or median point: use fun.y = mean or fun.y = median

e + geom_violin(trim = FALSE) +
stat_summary(fun.y = mean, geom = "point",
shape = 23, size = 2, color = "blue")

# Add mean points +/- SD

# Use geom = "pointrange" or geom = "crossbar"
e + geom_violin(trim = FALSE) +
stat_summary(fun.data="mean_sdl", fun.args = list(mult=1),
geom="pointrange", color = "red")

# Combine with box plot to add median and quartiles

e + geom_violin(trim = FALSE) +
geom_boxplot(width = 0.2)
16.3. CHANGE COLORS BY GROUPS 95

30 30 30
len

len

len
20 20 20

10 10 10

0.5 1 2 0.5 1 2 0.5 1 2

dose dose dose

The function mean_sdl is used for adding mean and standard deviation. It computes
the mean plus or minus a constant times the standard deviation. In the R code
above, the constant is specified using the argument mult (mult = 1). By default
mult = 2. The mean +/- SD can be added as a crossbar or a pointrange.

16.3 Change colors by groups

Violin plot outline and fill colors can be automatically controlled by the levels of the
grouping variable dose:

# Change outline colors by dose (groups)

e + geom_violin(aes(color = dose), trim = FALSE)

# Change fill color by dose (groups)

e + geom_violin(aes(fill = dose), trim = FALSE)

30 dose 30 dose
0.5 0.5
len

len

20 20
1 1

10 2 10 2

0.5 1 2 0.5 1 2
dose dose
As described in box plot chapter (Chapter 15), its possible to change manually violin
plot outline/fill colors, as follow:
96 CHAPTER 16. VIOLIN PLOTS

# Change manually outline colors

e2 <- e + geom_violin(aes(color = dose), trim = FALSE) + theme_minimal()
e2 + scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))

# Change manually fill colors

e3 <- e + geom_violin(aes(fill = dose), trim = FALSE) + theme_minimal()
e3 + scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))

30 dose 30 dose
0.5 0.5
len

20 len 20
1 1
10 2 10 2

0.5 1 2 0.5 1 2
dose dose
Read more on ggplot2 colors here: Chapter 26

16.4 Violin plots with multiple groups

The grouping variables dose and supp are used:

# Change colors by groups

e + geom_violin(aes(fill = supp), trim = FALSE)

# Change fill colors

e + geom_violin(aes(fill = supp), trim = FALSE) +
scale_fill_manual(values=c("#999999", "#E69F00"))

30 30
supp supp
len

len

20 OJ 20 OJ
VC VC
10 10

0.5 1 2 0.5 1 2
dose dose
Chapter 17

Dot Plots

The function geom_dotplot() is used to create a dot plot.

Key functions: geom_dotplot(), stat_summary()

Key arguments to customize the plot: alpha, color, dotsize and fill.

17.1 Basic dot plots

# Basic plot
e + geom_dotplot(binaxis = "y", stackdir = "center")

# Change dotsize and stack ratio

e + geom_dotplot(binaxis = "y", stackdir = "center",
stackratio = 1.5, dotsize = 1.1)

97
98 CHAPTER 17. DOT PLOTS

30 30
len

len
20 20

10 10

0.5 1 2 0.5 1 2
dose dose

To change the order of items (or to select some of the items), the function
scale_x_discrete() can be used as described in Chapter 15

17.2 Add summary statistics

The function stat_summary() can be used to add mean/median points and more
on a violin plot

# Add mean or median point: use fun.y = mean or fun.y = median

e + geom_dotplot(binaxis = "y", stackdir = "center") +
stat_summary(fun.y = mean, geom = "point",
shape = 18, size = 3, color = "red")

# Add mean points +/- SD

# Use geom = "pointrange" or geom = "crossbar"
e + geom_dotplot(binaxis = "y", stackdir = "center") +
stat_summary(fun.data="mean_sdl", fun.args = list(mult=1),
geom="pointrange", color = "red")
17.2. ADD SUMMARY STATISTICS 99

30 30
len

len
20 20

10 10

0.5 1 2 0.5 1 2
dose dose
Combine with box plot and dot plot:

# Combine with box plot

e + geom_boxplot() +
geom_dotplot(binaxis = "y", stackdir = "center")

# Combine with violin plot

e + geom_violin(trim = FALSE) +
geom_dotplot(binaxis='y', stackdir='center')

# Dot plot + violin plot + stat summary

e + geom_violin(trim = FALSE) +
geom_dotplot(binaxis='y', stackdir='center') +
stat_summary(fun.data="mean_sdl", fun.args = list(mult=1),
geom="pointrange", color = "red")

30 30 30
len

len

len

20 20 20

10 10 10

0.5 1 2 0.5 1 2 0.5 1 2

dose dose dose
100 CHAPTER 17. DOT PLOTS

17.3 Change colors by groups

Dot plot outline and fill colors can be automatically controlled by the levels of the
grouping variable dose:

# Use single colors

e + geom_dotplot(binaxis='y', stackdir='center', color = "black",
fill = "lightgray") + theme_minimal()

# Change outline colors by dose (groups)

e + geom_dotplot(aes(color = dose), binaxis='y', stackdir='center',
fill = "white") + theme_minimal()

# Change fill color by dose (groups)

e + geom_dotplot(aes(fill = dose), binaxis='y', stackdir='center') +
theme_minimal()

30 30 dose 30 dose
0.5 0.5
len

len

len
20 20 20
1 1
10 10 2 10 2

0.5 1 2 0.5 1 2 0.5 1 2

dose dose dose
As described in box plot chapter (Chapter 15), its possible to change manually dot
plot outline/fill colors, as follow:

# Change manually outline colors

# Use custom color palettes
e2 <- e + geom_dotplot(aes(color = dose), binaxis='y',
stackdir='center', fill = "white") + theme_minimal()
e2 + scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))

# Change manually fill colors

# Use custom color palettes
17.4. DOT PLOT WITH MULTIPLE GROUPS 101

e3 <- e + geom_dotplot(aes(fill = dose), binaxis='y',

stackdir='center') + theme_minimal()
e3 + scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))

30 dose 30 dose
0.5 0.5
len

len
20 20
1 1
10 2 10 2

0.5 1 2 0.5 1 2
dose dose
Read more on ggplot2 colors here: Chapter 26

17.4 Dot plot with multiple groups

The grouping variables dose and supp are used:

# Change colors by groups

e + geom_dotplot(aes(fill = supp), binaxis='y', stackdir='center')

# Change the position : interval between dot plot of the same group
e + geom_dotplot(aes(fill = supp), binaxis='y', stackdir='center',
position=position_dodge(0.8))

30 30

supp supp
len

len

20 OJ 20 OJ
VC VC

10 10

0.5 1 2 0.5 1 2
dose dose
102 CHAPTER 17. DOT PLOTS

Change dot plot colors and add box plots :

# Change colors
e + geom_dotplot(aes(fill = supp), binaxis='y', stackdir='center',
position=position_dodge(0.8)) +
scale_fill_manual(values=c("#999999", "#E69F00"))

# Add box plots

e + geom_boxplot(fill = "white") +
geom_dotplot(aes(fill = supp), binaxis='y', stackdir='center')

# Change the position

e + geom_boxplot(aes(fill = supp), position=position_dodge(0.8))+
geom_dotplot(aes(fill = supp), binaxis='y', stackdir='center',
position=position_dodge(0.8))

30 30
supp supp
len

len

20 OJ 20 OJ
VC VC
10 10

0.5 1 2 0.5 1 2
dose dose

30
supp
len

20 OJ
VC
10

0.5 1 2
dose
Chapter 18

Stripcharts

Stripcharts are also known as one dimensional scatter plots. These plots are suitable
compared to box plots when sample sizes are small.
The function geom_jitter() is used.

Key functions: geom_jitter(), stat_summary()

Key arguments to customize the plot: alpha, color, shape, size and fill.

18.1 Basic stripcharts

# Basic plot
e + geom_jitter()

# Change the position

# 0.2 : degree of jitter in x direction
e + geom_jitter(position = position_jitter(0.2))

# Change point shapes and size

e + geom_jitter(position=position_jitter(0.2),
shape=17, size = 1.2)

103
104 CHAPTER 18. STRIPCHARTS

30 30 30
len

len

len
20 20 20

10 10 10

0.5 1 2 0.5 1 2 0.5 1 2

dose dose dose
Read more on point shapes: Chapter 27.

18.2 Add summary statistics

The function stat_summary() can be used to add mean/median points and more
on a violin plot

# Add mean or median point: use fun.y = mean or fun.y = median

e + geom_jitter(position = position_jitter(0.2)) +
stat_summary(fun.y = mean, geom = "point",
shape = 18, size = 3, color = "red")

# Add mean points +/- SD

# Use geom = "pointrange" or geom = "crossbar"
e + geom_jitter(position = position_jitter(0.2))+
stat_summary(fun.data="mean_sdl", fun.args = list(mult=1),
geom="pointrange", color = "red")

30 30
len

len

20 20

10 10

0.5 1 2 0.5 1 2
dose dose
18.3. CHANGE POINT SHAPES BY GROUPS 105

Combine with box plot and violin plot:

# Combine with box plot

e + geom_boxplot() +
geom_jitter(position = position_jitter(0.2))

# Combine with violin plot

e + geom_violin(trim = FALSE) +
geom_jitter(position = position_jitter(0.2))

# Strip chart + violin plot + stat summary

e + geom_violin(trim = FALSE) +
geom_jitter(position = position_jitter(0.2)) +
stat_summary(fun.data="mean_sdl", fun.args = list(mult=1),
geom="pointrange", color = "red")

30 30 30
len

len

len

20 20 20

10 10 10

0.5 1 2 0.5 1 2 0.5 1 2

dose dose dose

18.3 Change point shapes by groups

In the R code below, point shapes are controlled automatically by the variable dose.
You can also set point shapes manually using the function scale_shape_manual()

# Change point shapes by groups

e + geom_jitter(aes(shape = dose), position=position_jitter(0.2))

# Change point shapes manually

106 CHAPTER 18. STRIPCHARTS

e + geom_jitter(aes(shape = dose), position=position_jitter(0.2)) +

scale_shape_manual(values=c(1, 17, 19))

30 30
dose dose
0.5 0.5
len

len
20 20
1 1
2 2
10 10

0.5 1 2 0.5 1 2
dose dose
Read more on point shapes : Chapter 27

18.4 Change colors by groups

Point colors can be automatically controlled by the levels of the grouping variable
dose:

# Use single colors

e + geom_jitter(position = position_jitter(0.2), color = "steelblue") +
theme_minimal()

# Change point colors by dose (groups)

e + geom_jitter(aes(color = dose), position = position_jitter(0.2)) +
theme_minimal()
18.4. CHANGE COLORS BY GROUPS 107

30 30
dose
0.5
len

len
20 20
1
2
10 10

0.5 1 2 0.5 1 2
dose dose
Change manually point 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

Change manually point colors:

# Use custom color palettes

e3 <- e + geom_jitter(aes(color = dose), position = position_jitter(0.2)) +
theme_minimal()
e3 + scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))

# Use brewer color palettes

e3 + scale_color_brewer(palette="Dark2")

30 30
dose dose
0.5 0.5
len

len

20 20
1 1
2 2
10 10

0.5 1 2 0.5 1 2
dose dose
Read more on ggplot2 colors here: Chapter 26
108 CHAPTER 18. STRIPCHARTS

18.5 Stripchart with multiple groups

The grouping variables dose and supp are used:

# Change colors and shapes by groups

e + geom_jitter(aes(color = supp, shape = supp),
position=position_jitter(0.2))

# Change the position : interval between dot plot of the same group
e + geom_jitter(aes(color = supp, shape = supp),
position=position_dodge(0.2))

30 30
supp supp
len

len

20 OJ 20 OJ
VC VC
10 10

0.5 1 2 0.5 1 2
dose dose
Change point plot colors and add box plots :

# Change colors
e + geom_jitter(aes(color = supp, shape = supp),
position=position_jitter(0.2))+
scale_color_manual(values=c("#999999", "#E69F00"))

# Add box plots

e + geom_boxplot(color = "black") +
geom_jitter(aes(color = supp, shape = supp),
position=position_jitter(0.2))

# Change the position

e + geom_boxplot(aes(color = supp), position=position_dodge(0.8)) +
geom_jitter(aes(color = supp, shape = supp),
position=position_dodge(0.8))
18.5. STRIPCHART WITH MULTIPLE GROUPS 109

30 30

supp supp
20 20
len

len
OJ OJ
VC VC

10 10

0.5 1 2 0.5 1 2
dose dose

30

supp
20
len

OJ
VC

10

0.5 1 2
dose
Chapter 19

Line Plots

In a line graph, observations are ordered by x value and connected.

x value (for x axis) can be :

date : for a time series data

texts
discrete numeric values
continuous numeric values

The functions geom_line(), geom_step() or geom_path() can be used to gener-

ate line plots.

Key functions: geom_line(), geom_step(), geom_path()

Key arguments to customize the plot: alpha, color, linetype and size.

19.1 Data format

Data derived from ToothGrowth data sets are used.

110
19.2. BASIC LINE PLOTS 111

df <- data.frame(dose=c("D0.5", "D1", "D2"),

len=c(4.2, 10, 29.5))

head(df)

## dose len
## 1 D0.5 4.2
## 2 D1 10.0
## 3 D2 29.5

df2 <- data.frame(supp=rep(c("VC", "OJ"), each=3),

dose=rep(c("D0.5", "D1", "D2"),2),
len=c(6.8, 15, 33, 4.2, 10, 29.5))

head(df2)

## supp dose len

## 1 VC D0.5 6.8
## 2 VC D1 15.0
## 3 VC D2 33.0
## 4 OJ D0.5 4.2
## 5 OJ D1 10.0
## 6 OJ D2 29.5

len : Tooth length

dose : Dose in milligrams (0.5, 1, 2)
supp : Supplement type (VC or OJ)

19.2 Basic line plots

p <- ggplot(data=df, aes(x=dose, y=len, group=1))

# Basic line plot with points
p + geom_line() + geom_point()
112 CHAPTER 19. LINE PLOTS

# Change line type and color

p + geom_line(linetype = "dashed", color = "steelblue")+
geom_point(color = "steelblue")

# Use geom_step()
p + geom_step() + geom_point()

30 30 30

20 20 20
len

len

len
10 10 10

D0.5 D1 D2 D0.5 D1 D2 D0.5 D1 D2

dose dose dose
Read more on line types : Chapter 28

geom_line() : Connect observations, ordered by x value

geom_path() : Observations are connected in original order
geom_step() : Connect observations by stairs

19.3 Line plot with multiple groups

In the graphs below, line types and point shapes are controlled automatically by the
levels of the variable supp :

p <- ggplot(df2, aes(x=dose, y=len, group=supp))

# Change line types and point shapes by groups
p + geom_line(aes(linetype = supp)) +
geom_point(aes(shape = supp))

# Change line types, point shapes and colors

p + geom_line(aes(linetype=supp, color = supp))+
geom_point(aes(shape=supp, color = supp))
19.4. LINE PLOT WITH A NUMERIC X-AXIS 113

# Change color manually: custom color

p + geom_line(aes(linetype=supp, color = supp))+
geom_point(aes(shape=supp, color = supp)) +
scale_color_manual(values=c("#999999", "#E69F00"))

30 30

supp supp
20 20
len

len
OJ OJ
VC VC

10 10

D0.5 D1 D2 D0.5 D1 D2
dose dose

30

supp
20
len

OJ
VC

10

D0.5 D1 D2
dose

Read more on line types: Chapter 28

Read more on point shapes: Chapter 27
Read more on ggplot2 colors: Chapter 26

19.4 Line plot with a numeric x-axis

If the variable on x-axis is numeric, it can be useful to treat it as a continuous or a
factor variable depending on what you want to do:
114 CHAPTER 19. LINE PLOTS

# Create some data

df3 <- data.frame(supp=rep(c("VC", "OJ"), each=3),
dose=rep(c("0.5", "1", "2"),2),
len=c(6.8, 15, 33, 4.2, 10, 29.5))
head(df3)

## supp dose len

## 1 VC 0.5 6.8
## 2 VC 1 15.0
## 3 VC 2 33.0
## 4 OJ 0.5 4.2
## 5 OJ 1 10.0
## 6 OJ 2 29.5

# x axis treated as continuous variable

df3$dose <- as.numeric(as.vector(df3$dose))
ggplot(data=df3, aes(x = dose, y = len, group = supp, color = supp)) +
geom_line() + geom_point()

# Axis treated as discrete variable

df2$dose<-as.factor(df3$dose)
ggplot(data=df2, aes(x = dose, y = len, group = supp, color = supp)) +
geom_line() + geom_point()

30 30

supp supp
20 20
len

len

OJ OJ
VC VC

10 10

0.5 1.0 1.5 2.0 0.5 1 2

dose dose
19.5. LINE PLOT WITH DATES ON X-AXIS: TIME SERIES 115

19.5 Line plot with dates on x-axis: Time series

economics time series data sets are used :

head(economics)

## Source: local data frame [6 x 6]

##
## date pce pop psavert uempmed unemploy
## (date) (dbl) (int) (dbl) (dbl) (int)
## 1 1967-07-01 507.4 198712 12.5 4.5 2944
## 2 1967-08-01 510.5 198911 12.5 4.7 2945
## 3 1967-09-01 516.3 199113 11.7 4.6 2958
## 4 1967-10-01 512.9 199311 12.5 4.9 3143
## 5 1967-11-01 518.1 199498 12.5 4.7 3066
## 6 1967-12-01 525.8 199657 12.1 4.8 3018

Plots :

# Basic line plot

ggplot(data=economics, aes(x = date, y = pop))+
geom_line()

# Plot a subset of the data

ss <- subset(economics, date > as.Date("2006-1-1"))
ggplot(data = ss, aes(x = date, y = pop)) + geom_line()

320000 320000

315000
280000
pop

pop

310000

240000 305000

300000
200000
1970 1980 1990 2000 2010 2006 2008 2010 2012 2014
date date
Change line size :
116 CHAPTER 19. LINE PLOTS

# Change line size

ggplot(data = economics, aes(x = date, y = pop, size = unemploy/pop)) +
geom_line()

320000

unemploy/pop
280000 0.02
pop

0.03
0.04
240000
0.05

200000
1970 1980 1990 2000 2010
date
Plot multiple time series data:

# Solution 1
ggplot(economics, aes(x=date)) +
geom_line(aes(y = psavert), color = "darkred") +
geom_line(aes(y = uempmed), color="steelblue", linetype="twodash") +
theme_minimal()

25
20
psavert

15
10
5

1970 1980 1990 2000 2010

date
19.5. LINE PLOT WITH DATES ON X-AXIS: TIME SERIES 117

# Solution 2: melt by date.

require(reshape2)
df <- melt(economics[, c("date", "psavert", "uempmed")], id="date")
ggplot(df, aes(x = date, y = value)) +
geom_line(aes(color = variable), size=1) +
scale_color_manual(values = c("#999999", "#E69F00")) +
theme_minimal()

25
20 variable
value

15 psavert
10 uempmed
5

1970 1980 1990 2000 2010

date

# Area plot
ggplot(economics, aes(x=date)) +
geom_area(aes(y=psavert), fill = "#999999",
color = "#999999", alpha=0.5) +
geom_area(aes(y=uempmed), fill = "#E69F00",
color = "#E69F00", alpha=0.5) +
theme_minimal()

25
20
psavert

15
10
5
0

1970 1980 1990 2000 2010

date
Chapter 20

Bar Plots

The function geom_bar() can be used to create a bar plot.

Key function: geom_bar()

Key arguments to customize the plot: alpha, color, fill, linetype and size.

20.1 Data format

Well use the same data sets df and df2 described in Chapter 19.
Data derived from ToothGrowth data sets are used.

df <- data.frame(dose=c("D0.5", "D1", "D2"),

len=c(4.2, 10, 29.5))

# head(df)

df2 <- data.frame(supp=rep(c("VC", "OJ"), each=3),

dose=rep(c("D0.5", "D1", "D2"),2),
len=c(6.8, 15, 33, 4.2, 10, 29.5))

# head(df2)

118
20.2. BASIC BAR PLOTS 119

20.2 Basic bar plots

We start by creating a simple bar plot (named f ) using the df data set:

f <- ggplot(df, aes(x = dose, y = len))

# Basic bar plot

f + geom_bar(stat = "identity")

# Change fill color and add labels at the top (vjust = -0.3)
f + geom_bar(stat = "identity", fill = "steelblue")+
geom_text(aes(label = len), vjust = -0.3, size = 3.5)+
theme_minimal()

# Label inside bars, vjust = 1.6

f + geom_bar(stat="identity", fill="steelblue")+
geom_text(aes(label=len), vjust=1.6, color="white", size=3.5)+
theme_minimal()

30 30 29.5 30
29.5

20 20 20
len

len
len

10
10 10
10 10
4.2
4.2
0 0
0
D0.5 D1 D2 D0.5 D1 D2 D0.5 D1 D2
dose dose dose

Its possible to change the width of bars using the argument width (e.g.: width =
0.5)

To change the order of items (or to select some of the items), the function
scale_x_discrete() can be used as described in Chapter 15
120 CHAPTER 20. BAR PLOTS

20.3 Change color by groups

# Change bar plot line colors by groups

f + geom_bar(aes(color = dose), stat="identity", fill="white")

# Change bar plot fill colors by groups

f + geom_bar(aes(fill = dose), stat="identity")

# Change outline color manually: custom color

f + geom_bar(aes(color = dose), stat="identity", fill="white") +
scale_color_manual(values = c("#999999", "#E69F00", "#56B4E9"))

# Change fill color manually: custom color

f + geom_bar(aes(fill = dose), stat="identity") +
scale_fill_manual(values = c("#999999", "#E69F00", "#56B4E9"))

30 30

dose dose
20 20
D0.5 D0.5
len

len

D1 D1
10 10
D2 D2

0 0
D0.5 D1 D2 D0.5 D1 D2
dose dose
30 30

dose dose
20 20
D0.5 D0.5
len

len

D1 D1
10 10
D2 D2

0 0
D0.5 D1 D2 D0.5 D1 D2
dose dose
20.4. BAR PLOT WITH MULTIPLE GROUPS 121

20.4 Bar plot with multiple groups

g <- ggplot(data=df2, aes(x=dose, y=len, fill=supp))

# Stacked bar plot

g + geom_bar(stat = "identity")

# Use position=position_dodge()
g + geom_bar(stat="identity", position=position_dodge())

60
30

40
supp supp
20
len

len
OJ OJ

20 VC VC
10

0 0
D0.5 D1 D2 D0.5 D1 D2
dose dose
Add labels to a dodged bar plot :

ggplot(data=df2, aes(x=dose, y=len, fill=supp)) +

geom_bar(stat="identity", position = position_dodge())+
geom_text(aes(label = len), vjust = 1.6, color = "white",
position = position_dodge(0.9), size = 3.5)

30 33
29.5
supp
20
len

OJ
15 VC
10
10
6.8
0 4.2
D0.5 D1 D2
dose
Add labels to a stacked bar plot: 3 steps are required
122 CHAPTER 20. BAR PLOTS

1. Sort the data by dose and supp : the package plyr is used
2. Calculate the cumulative sum of the variable len for each dose
3. Create the plot

require(plyr)
# Sort by dose and supp
df_sorted <- arrange(df2, dose, supp)
head(df_sorted)

## supp dose len

## 1 OJ D0.5 4.2
## 2 VC D0.5 6.8
## 3 OJ D1 10.0
## 4 VC D1 15.0
## 5 OJ D2 29.5
## 6 VC D2 33.0

# Calculate the cumulative sum of len for each dose

df_cumsum <- ddply(df_sorted, "dose", transform,
label_ypos=cumsum(len))
head(df_cumsum)

## supp dose len label_ypos

## 1 OJ D0.5 4.2 4.2
## 2 VC D0.5 6.8 11.0
## 3 OJ D1 10.0 10.0
## 4 VC D1 15.0 25.0
## 5 OJ D2 29.5 29.5
## 6 VC D2 33.0 62.5

# Create the bar plot

ggplot(data=df_cumsum, aes(x = dose, y = len, fill = supp)) +
geom_bar(stat = "identity")+
geom_text(aes(y = label_ypos, label = len), vjust=1.6,
color = "white", size = 3.5)
20.4. BAR PLOT WITH MULTIPLE GROUPS 123

60 33

40 supp
len

OJ
29.5 VC
20 15

6.8 10
0 4.2
D0.5 D1 D2
dose
If you want to place the labels at the middle of bars, you have to modify the cumulative
sum as follow :

df_cumsum <- ddply(df_sorted, "dose", transform,

label_ypos = cumsum(len) - 0.5*len)

# Create the bar plot

ggplot(data=df_cumsum, aes(x = dose, y = len, fill = supp)) +
geom_bar(stat = "identity")+
geom_text(aes(y = label_ypos, label = len), vjust = 1.6,
color = "white", size = 3.5)

60

40 33 supp
len

OJ
VC
20
15
29.5
6.8
0 10
4.2
D0.5 D1 D2
dose
Chapter 21

Visualizing Error

21.1 Data format

The ToothGrowth data set well be used. We start by creating a data set named df
which holds ToothGrowth data.

# ToothGrowth data set

df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)

## len supp dose

## 1 4.2 VC 0.5
## 2 11.5 VC 0.5
## 3 7.3 VC 0.5

21.2 Compute mean and standard deviation

Using dplyr package, the following R code creates a data set named df2 which holds
the mean and the SD of tooth length (len) by groups (dose).

124
21.3. PLOT TYPES 125

library("dplyr")
df2 <- df %>%
group_by(dose) %>%
summarise(
sd = sd(len),
len = mean(len)
)

head(df2)

## Source: local data frame [3 x 3]

##
## dose sd len
## (fctr) (dbl) (dbl)
## 1 0.5 4.499763 10.605
## 2 1 4.415436 19.735
## 3 2 3.774150 26.100

21.3 Plot types

We start by creating a plot, named f, that well finish in the next section by adding a
layer.

f <- ggplot(df2, aes(x = dose, y = len,

ymin = len-sd, ymax = len+sd))

Possible layers include:

geom_crossbar() for hollow bar with middle indicated by horizontal line

geom_errorbar() for error bars
geom_errorbarh() for horizontal error bars
geom_linerange() for drawing an interval represented by a vertical line
geom_pointrange() for creating an interval represented by a vertical line,
with a point in the middle.
126 CHAPTER 21. VISUALIZING ERROR

f + geom_crossbar() f + geom_errorbar() f + geom_linerange() f + geom_pointrange()

dose dose dose dose

21.4 Cross bar

Cross bar is a hollow bar with middle indicated by horizontal line.

Key function: geom_crossbar(), stat_summary()

Key arguments to customize the plot: alpha, color, fill, linetype and size.

Well use the data set named df2, which holds the mean and the SD of tooth length
(len) by groups (dose).

# Default plot
f + geom_crossbar()

# color by groups
f + geom_crossbar(aes(color = dose))

# Change color manually

f + geom_crossbar(aes(color = dose)) +
scale_color_manual(values = c("#999999", "#E69F00", "#56B4E9"))+
theme_minimal()

# fill by groups and change color manually

f + geom_crossbar(aes(fill = dose)) +
scale_fill_manual(values = c("#999999", "#E69F00", "#56B4E9"))+
theme_minimal()
21.4. CROSS BAR 127

30 30

25 25 dose
20 20 0.5
len

len
1
15 15
2
10 10

5 5
0.5 1 2 0.5 1 2
dose dose
30 30
25 dose 25 dose
20 0.5 20 0.5
len

len
15 1 15 1

10 2 10 2

5 5

0.5 1 2 0.5 1 2
dose dose
Cross bar with multiple groups: we start by creating a data set named df3 which
holds the mean and the SD of tooth length (len) by 2 groups (supp and dose).

library("dplyr")
df3 <- df %>%
group_by(supp, dose) %>%
summarise(
sd = sd(len),
len = mean(len)
)
head(df3)

## Source: local data frame [3 x 4]

## Groups: supp [1]
##
## supp dose sd len
## (fctr) (fctr) (dbl) (dbl)
## 1 OJ 0.5 4.459709 13.23
## 2 OJ 1 3.910953 22.70
## 3 OJ 2 2.655058 26.06
128 CHAPTER 21. VISUALIZING ERROR

The data set df3 is used to create cross bars with multiple groups. For this end,
the variable len is plotted by dose and the color is changed by the levels of the factor
supp.

f <- ggplot(df3, aes(x = dose, y = len,

ymin = len-sd, ymax = len+sd))
# Default plot
f + geom_crossbar(aes(color = supp))

# Use position_dodge() to avoid overlap

f + geom_crossbar(aes(color = supp),
position = position_dodge(1))

30 30

supp supp
20 20
len

len

OJ OJ
VC VC
10 10

0.5 1 2 0.5 1 2
dose dose

A simple alternative to geom_crossbar() is to use the function stat_summary()

as follow. In this case, the mean and the SD can be computed automatically.

f <- ggplot(df, aes(x = dose, y = len, color = supp))

# Use geom_crossbar()
f + stat_summary(fun.data="mean_sdl", fun.args = list(mult=1),
geom="crossbar", width = 0.6,
position = position_dodge(0.8))
21.5. ERROR BAR 129

21.5 Error bar

Key functions: geom_errorbar(), stat_summary()

Key arguments to customize the plot: alpha, color, linetype, size and
width.

Well use the data set named df2, which holds the mean and the SD of tooth length
(len) by groups (dose).
We start by creating a plot, named f, that well finish next by adding a layer.

f <- ggplot(df2, aes(x = dose, y = len,

ymin = len-sd, ymax = len+sd))

# Error bars colored by groups

f + geom_errorbar(aes(color = dose), width = 0.2)

# Combine with line plot

f + geom_line(aes(group = 1)) +
geom_errorbar(width = 0.2)

# Combine with bar plot, color by groups

f + geom_bar(aes(color = dose), stat = "identity", fill ="white") +
geom_errorbar(aes(color = dose), width = 0.2)

# Keep only upper error bars

f + geom_bar(aes(color = dose), stat="identity", fill ="white") +
geom_errorbar(aes(color = dose, ymin = len), width=.2)
130 CHAPTER 21. VISUALIZING ERROR

30 30 30

25 dose 25 dose
20
20 0.5 20 0.5
len

len

len
1 1
15 15 10
2 2
10 10
0
5 5
0.5 1 2 0.5 1 2 0.5 1 2
dose dose dose
30

dose
20
0.5
len

1
10
2

0
0.5 1 2
dose

In the R code above, the argument width specifies the width of error bars.

Error bars with multiple groups:

The data set df3 is used to create cross bars with multiple groups. For this end,
the variable len is plotted by dose and the color is changed by the levels of the factor
supp.

f <- ggplot(df3, aes(x = dose, y = len,

ymin = len-sd, ymax = len+sd))
# Bar plot with error bar
f + geom_bar(aes(fill = supp), stat = "identity",
position = "dodge") +
geom_errorbar(aes(color = supp), position = "dodge")

# Line plot with error bar

f + geom_line(aes(group = supp, color = supp)) +
geom_point(aes(color = supp))+
geom_errorbar(aes(color = supp), width=.2,
position = position_dodge(0.05))
21.6. HORIZONTAL ERROR BAR 131

30 30

20 supp supp
20
len

len
OJ OJ
VC VC
10

10

0
0.5 1 2 0.5 1 2
dose dose

You can also use the functions geom_pointrange() or geom_linerange() instead

of using geom_errorbar()

21.6 Horizontal error bar

Key function: geom_errorbarh()

Key arguments to customize the plot: alpha, color, linetype, size and
height.

Well use the data set named df2, which holds the mean and the SD of tooth length
(len) by groups (dose).
We start by creating a plot, named f, that well finish next by adding a layer.

The arguments xmin and xmax are used for horizontal error bars.

f <- ggplot(df2, aes(x = len, y = dose ,

xmin = len-sd, xmax = len+sd))
132 CHAPTER 21. VISUALIZING ERROR

2 2 dose
0.5
dose

dose
1 1
1
2
0.5 0.5

5 10 15 20 25 30 5 10 15 20 25 30
len len

21.7 Interval represented by a vertical line

Key functions: geom_linerange(), geom_pointrange()

Key arguments to customize the plot: alpha, color, linetype, size, shape
and fill (for geom_pointrange()).

geom_linerange(): Add an interval represented by a vertical line

geom_pointrange(): Add an interval represented by a vertical line with a
point in the middle

Well use the data set df2.

f <- ggplot(df2, aes(x = dose, y = len,

ymin=len-sd, ymax=len+sd))
# Line range
f + geom_linerange()

# Point range
f + geom_pointrange()
21.8. COMBINE DOT PLOT AND ERROR BARS 133

30 30

25 25

20 20
len

len
15 15

10 10

5 5
0.5 1 2 0.5 1 2
dose dose

21.8 Combine dot plot and error bars

Key functions: geom_errorbarh(), geom_errorbar(), geom_linerange(),

geom_pointrange(), geom_crossbar(), stat_summary()

Key arguments to customize the plot: alpha, color, fill, linetype and
size.

To combine geom_dotplot() and error bars, well use the ToothGrowth data
set. You dont need to compute the mean and SD. This can be done automatically by
using the function stat_summary() in combination with the argument fun.data
= mean_sdl.
We start by creating a dot plot, named g, that well finish in the next section by
adding error bar layers.

g <- ggplot(df, aes(x=dose, y=len)) +

geom_dotplot(binaxis='y', stackdir='center')

# use geom_crossbar()
g + stat_summary(fun.data="mean_sdl", fun.args = list(mult=1),
geom="crossbar", width=0.5)

# Use geom_errorbar()
134 CHAPTER 21. VISUALIZING ERROR

g + stat_summary(fun.data=mean_sdl, fun.args = list(mult=1),

geom="errorbar", color="red", width=0.2) +
stat_summary(fun.y=mean, geom="point", color="red")

# Use geom_pointrange()
g + stat_summary(fun.data=mean_sdl, fun.args = list(mult=1),
geom="pointrange", color="red")

30 30 30
len

len

len
20 20 20

10 10 10

0.5 1 2 0.5 1 2 0.5 1 2

dose dose dose
Chapter 22

Pie Charts

The function coord_polar() is used to produce a pie chart, which is just a stacked
bar chart in polar coordinates.

22.1 Basic pie charts

Create some data :

df <- data.frame(
group = c("Male", "Female", "Child"),
value = c(25, 25, 50))
head(df)

## group value
## 1 Male 25
## 2 Female 25
## 3 Child 50

Create a pie chart :

# default plot
p <- ggplot(df, aes(x="", y = value, fill=group)) +
geom_bar(width = 1, stat = "identity") +

135
136 CHAPTER 22. PIE CHARTS

coord_polar("y", start=0)
p

# Use custom fill color palettes

p + scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))

0/100 0/100

group group
Child Child
75 25 75 25
x

x
Female Female
Male Male

50 50

value value

22.2 Customized pie charts

Create a blank theme :

blank_theme <- theme_minimal()+

theme(
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.text.x=element_blank(),
panel.border = element_blank(),
panel.grid=element_blank(),
axis.ticks = element_blank(),
plot.title=element_text(size=14, face="bold")
)

1. Apply the blank theme

2. Remove axis tick mark labels
3. Add text annotations : The package scales is used to format the labels in
percent
22.2. CUSTOMIZED PIE CHARTS 137

# Apply blank theme

require(scales)
p + scale_fill_brewer("Blues") + blank_theme +
geom_text(aes(y = value/3 + c(0, cumsum(value)[-length(value)]),
label = percent(value/100)), size=5)

25%
Blues
Child
Female

50% 25% Male

In the R code above, we used the function scale_fill_brewer() to change fill colors.
You can read more about colors in Chapter 26
 Part V

Graphical Parameters

138
Chapter 23

Graphical Primitives

This section describes how to add graphical elements (polygon, path, ribbon,
segment and rectangle) to a plot.

Key functions: geom_path(), geom_ribbon(), geom_rect(), geom_segment()

Key arguments to customize the plot: alpha, color, fill (for ribbon only),
linetype and size

The functions below well be used:

geom_polygon(): Add polygon, a filled path

geom_path(): Connect observations in original order

geom_ribbon(): Add ribbons, y range with continuous x values.

geom_segment(): Add a single line segments

geom_curve(): Add curves

geom_rect(): Add a 2d rectangles.

1. The R code below draws France map using geom_polygon():

139
140 CHAPTER 23. GRAPHICAL PRIMITIVES

require(maps)
france = map_data('world', region = 'France')
ggplot(france, aes(x = long, y = lat, group = group)) +
geom_polygon(fill = 'white', colour = 'black')

50
48
lat

46
44
42

-5 0 5 10
long

2. Use econimics data [in ggplot2] and produces path, ribbon and rectangles.

h <- ggplot(economics, aes(date, unemploy))

# Path
h + geom_path(size = 0.8, color = "#E46726") +
theme_minimal()
unemploy

12000
8000
4000

1970 1980 1990 2000 2010

date

# Combine path, ribbon and rectangle

h + geom_rect(aes(xmin = as.Date('1980-01-01'), ymin = -Inf,
xmax = as.Date('1985-01-01'), ymax = Inf),
fill = "#A29B32", color = "#D8DA9E", size =1.5) +
geom_ribbon(aes(ymin = unemploy-900, ymax = unemploy+900),
fill = "#F3BF94") +
geom_path(size = 0.8, color = "#E46726") +
theme_minimal()
 141

unemploy 16000
12000
8000
4000

1970 1980 1990 2000 2010

date

3. Add line segments and curves between points (x1, y1) and (x2, y2):

# Create a scatter plot

i <- ggplot(mtcars, aes(wt, mpg)) + geom_point()

# Add segment
i + geom_segment(aes(x = 2, y = 15, xend = 3, yend = 15))

# Add arrow
require(grid)
i + geom_segment(aes(x = 5, y = 30, xend = 3.5, yend = 25),
arrow = arrow(length = unit(0.5, "cm")))

# Add curves
i + geom_curve(aes(x = 2, y = 15, xend = 3, yend = 15))

35 35 35

30 30 30

25 25 25
mpg

mpg

mpg

20 20 20

15 15 15

10 10 10
2 3 4 5 2 3 4 5 2 3 4 5
wt wt wt
Chapter 24

Main Titles, Axis Labels and

Legend Title

Key functions: ggtitle(), xlab(), ylab(), labs()

We start by creating a box plot using the data set ToothGrowth:

# Convert the variable dose from numeric to factor variable

ToothGrowth$dose <- as.factor(ToothGrowth$dose)
p <- ggplot(ToothGrowth, aes(x=dose, y=len, fill = dose)) + geom_boxplot()

The function below can be used for changing titles and labels:

p + ggtitle("Main title"): Adds a main title above the plot

p + xlab("X axis label"): Changes the X axis label
p + ylab("Y axis label"): Changes the Y axis label
p + labs(title = "Main title", x = "X axis label", y = "Y axis label"):
Changes main title and axis labels

The function labs() can be also used to change the legend title.

142
24.1. CHANGE THE MAIN TITLE AND AXIS LABELS 143

24.1 Change the main title and axis labels

# Default plot
print(p)

# Change title and axis labels

p <- p +labs(title="Plot of length \n by dose",
x ="Dose (mg)", y = "Teeth length")
p

Plot of length
30 by dose
dose
dose
Teeth length

0.5 30
len

20
1 0.5
20
2 1
10
10 2

0.5 1 2 0.5 1 2
dose Dose (mg)

Note that, you can use \n, to split long title into multiple lines.

Plot titles can be also changed using the functions ggtitle(), xlab(), ylab() as follow.

p + ggtitle("Plot of length \n by dose") +

xlab("Dose (mg)") + ylab("Teeth length")

24.2 Change the appearance of labels

To change the appearance (color, size and face ) of labels, the functions theme()
and element_text() can be used.
The function element_blank() hides the labels.
144 CHAPTER 24. MAIN TITLES, AXIS LABELS AND LEGEND TITLE

# Change the appearance of labels.

# Values for face are one of "plain", "italic", "bold" and "bold.italic"
p + theme(
plot.title = element_text(color="red", size=12, face="bold.italic"),
axis.title.x = element_text(color="blue", size=12, face="bold"),
axis.title.y = element_text(color="#993333", size=12, face="bold")
)
# Hide labels
p + theme(plot.title = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank())

Plot of length
by dose 30
dose
Teeth length

dose
30 0.5
0.5 20
20 1
1
10 2
2 10
0.5 1 2
Dose (mg) 0.5 1 2

24.3 Change legend titles

labs() and scale functions (fill, color, size, shape, . . . ) are used to update legend
titles.

p + labs(fill = "Dose (mg)")

Plot of length
by dose Dose (mg)
Teeth length

30
0.5
20
1
10
2
0.5 1 2
Dose (mg)
Chapter 25

Legend Position and Appearance

Key functions: guides(), guide_legend() and guide_colourbar().

Create a box plot

# Convert the variable dose from numeric to factor variable

ToothGrowth$dose <- as.factor(ToothGrowth$dose)
p <- ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose))+
geom_boxplot()

25.1 Change legend position and appearance

1. Change legend position and appearance

# Change legend position: "left","top", "right", "bottom", "none"

p + theme(legend.position="top")

# Legend position as numeric vector c(x, y)

p + theme(legend.position = c(0.8, 0.2))

145
146 CHAPTER 25. LEGEND POSITION AND APPEARANCE

# Remove legends
p + theme(legend.position = "none")

dose 0.5 1 2 30 30

30

len

len
20 20
dose
len

20
0.5
10 10
10 1
2
0.5 1 2 0.5 1 2 0.5 1 2
dose dose dose

As shown above, the argument legend.position can be also a numeric vector c(x,y),
where x and y are the coordinates of the legend box. Their values should be between
0 and 1. c(0,0) corresponds to the "bottom left" and c(1,1) corresponds to the "top
right" position.

# Change the appearance of legend title and labels

p + theme(legend.title = element_text(colour="blue"),
legend.text = element_text(colour="red"))

# Change legend box background color

p + theme(legend.background = element_rect(fill="lightblue"))

30 dose 30 dose
0.5 0.5
len

len

20 20
1 1

10 2 10 2

0.5 1 2 0.5 1 2
dose dose

2. Customize legends using scale functions

25.2. GUIDES() : SET OR REMOVE THE LEGEND FOR A SPECIFIC AESTHETIC147

Change the order of legend items: scale_x_discrete()

Set legend title and labels: scale_fill_discrete()

# Change the order of legend items

p + scale_x_discrete(limits=c("2", "0.5", "1"))

# Set legend title and labels

p + scale_fill_discrete(name = "Dose", labels = c("A", "B", "C"))

30 dose 30 Dose
0.5 A
len

len

20 20
1 B

10 2 10 C

2 0.5 1 0.5 1 2
dose dose

25.2 guides() : set or remove the legend for a spe-

cific aesthetic
Its possible to use the function guides() to set or remove the legend of a particular
aesthetic (fill, color, size, shape, etc).

1. Prepare the data

# convert cyl and gear to factor variables

mtcars$cyl<-as.factor(mtcars$cyl)
mtcars$gear <- as.factor(mtcars$gear)

2. Create a scatter plot with multiple aesthetics (guides)

The color and the shape of the points are determined by the factor variables cyl and
gear, respectively. The size of the points are controlled by the variable qsec.
The function guide_legend() is used to change the order of guides.
148 CHAPTER 25. LEGEND POSITION AND APPEARANCE

# Plot with multiple aesthetics

p <- ggplot(data = mtcars,
aes(x = mpg, y = wt, color = cyl, size = qsec, shape = gear))+
geom_point()
p

# Change the order of guides using guide_legend()

p + guides(color = guide_legend(order=1),
size = guide_legend(order=2),
shape = guide_legend(order=3))

# Remove a legend for a particular aesthetic (color and size)

p+guides(color = FALSE, size = FALSE)

8 8
5 5
5
gear qsec
4 3 4 15.0 gear
4
4 17.5 3
wt

wt

wt

5 20.0 4
3 3
3
22.5 5
qsec
2 2
2
15.0 gear
10 15 20 25 30 35 17.5 10 15 20 25 30 35 3
10 15 20 25 30 35
mpg 20.0 mpg 4 mpg

Note that, in the case of continuous color, the function guide_colourbar() should
be used to change the order of color guide.

# Case of continuous color: Use guide_colourbar()

qplot(data = mpg, x = displ, y = cty, size = hwy,
colour = cyl, shape = drv) +
guides(colour = guide_colourbar(order = 1),
alpha = guide_legend(order = 2),
size = guide_legend(order = 3))
25.2. GUIDES() : SET OR REMOVE THE LEGEND FOR A SPECIFIC AESTHETIC149

Removing a particular legend can be done also when using the functions scale_xx.
In this case the argument guide is used as follow.

# Remove legend for the point shape

p + scale_shape(guide=FALSE)
# Remove legend for size
p + scale_size(guide=FALSE)
# Remove legend for color
p + scale_color_manual(values=c('#999999','#E69F00','#56B4E9'),
guide=FALSE)
Chapter 26

Colors

This chapter describes how to change the color of a graph. A color can be specified
either by name (e.g.: red) or by hexadecimal code (e.g. : #FF1234).
You will learn how to :

change colors by groups (automatically and manually)

use RColorBrewer and Wes Anderson color palettes
use gradient colors

ToothGrowth and mtcars data sets are used in the examples below.

# Convert dose and cyl columns from numeric to factor variables

ToothGrowth$dose <- as.factor(ToothGrowth$dose)
mtcars$cyl <- as.factor(mtcars$cyl)

We start by creating some plots which will be finished hereafter:

# Box plot
bp <- ggplot(ToothGrowth, aes(x=dose, y=len))

# Scatter plot
sp <- ggplot(mtcars, aes(x=wt, y=mpg))

150
26.1. USE A SINGLE COLOR 151

26.1 Use a single color

Change fill and outline colors

# box plot
bp + geom_boxplot(fill = 'steelblue', color = "red")

# scatter plot
sp + geom_point(color = 'darkblue')

35
30 30

25
mpg
len

20
20

10 15

10
0.5 1 2 2 3 4 5
dose wt

26.2 Change colors by groups

1. Changes colors by groups using the levels of dose variable :

# Box plot
bp <- bp + geom_boxplot(aes(fill = dose))
bp

# Scatter plot
sp <- sp + geom_point(aes(color = cyl))
sp
152 CHAPTER 26. COLORS

35
30 dose 30 cyl
0.5 25 4

mpg
len

20
1 20 6

10 2 15 8

10
0.5 1 2 2 3 4 5
dose wt

The lightness (l) and the chroma (c, intensity of color) of the default (hue) colors
can be modified using the functions scale_hue as follow.

# Box plot
bp + scale_fill_hue(l=40, c=35)

# Scatter plot
sp + scale_color_hue(l=40, c=35)

35
30 dose 30 cyl
0.5 25 4
mpg
len

20
1 20 6

10 2 15 8

10
0.5 1 2 2 3 4 5
dose wt

Note that, the default values for l and c are : l = 65, c = 100.

2. Change colors manually usin a custom color palettes:

scale_fill_manual() for box plot, bar plot, violin plot, dot plot, etc
scale_color_manual() for lines and points
26.2. CHANGE COLORS BY GROUPS 153

# Box plot
bp + scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))

# Scatter plot
sp + scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))

35
30 dose 30 cyl
0.5 25 4
mpg
len

20
1 20 6

10 2 15 8

10
0.5 1 2 2 3 4 5
dose wt

3. Use RColorBrewer palettes

scale_fill_brewer() for box plot, bar plot, violin plot, dot plot, etc
scale_color_brewer() for lines and points

# Box plot
bp + scale_fill_brewer(palette="Dark2")

# Scatter plot
sp + scale_color_brewer(palette="Dark2")

35
30 dose 30 cyl
0.5 25 4
mpg
len

20
1 20 6

10 2 15 8

10
0.5 1 2 2 3 4 5
dose wt
The available color palettes in the RColorBrewer package are :
154 CHAPTER 26. COLORS

4. Use Wes Anderson color palettes

Install and load the color palettes as follow :

# Install
install.packages("wesanderson")
# Load
library(wesanderson)

The available color palettes are :

26.2. CHANGE COLORS BY GROUPS 155

library(wesanderson)
# Box plot
bp+scale_fill_manual(values=wes_palette(n=3, name="GrandBudapest"))

# Scatter plot
sp+scale_color_manual(values=wes_palette(n=3, name="GrandBudapest"))

35
30 dose 30 cyl
0.5 mpg 25 4
len

20
1 20 6

10 2 15 8

10
0.5 1 2 2 3 4 5
dose wt

5. Use gray color palettes:

scale_fill_grey() for box plot, bar plot, violin plot, dot plot, etc
scale_colour_grey() for points, lines, etc

# Box plot
bp + scale_fill_grey(start=0.8, end=0.2) + theme_minimal()

# Scatter plot
sp + scale_color_grey(start=0.8, end=0.2) + theme_minimal()

35
30 dose 30 cyl
0.5 25 4
mpg
len

20
1 20 6
10 2 15 8
10

0.5 1 2 2 3 4 5
dose wt
156 CHAPTER 26. COLORS

26.3 Gradient or continuous colors

Plots can be colored according to the values of a continuous variable using the functions
:

scale_color_gradient(), scale_fill_gradient() for sequential gradients be-

tween two colors
scale_color_gradient2(), scale_fill_gradient2() for diverging gradients
scale_color_gradientn(), scale_fill_gradientn() for gradient between n
colors

26.3.1 Gradient between two colors

The graphs are colored using the qsec continuous variable :

# Color by qsec values

sp2 <- ggplot(mtcars, aes(x = wt, y = mpg)) +
geom_point(aes(color = qsec))
sp2

# Change the low and high colors

# Sequential color scheme
sp2+scale_color_gradient(low="blue", high="red")

# Diverging color scheme

mid <- mean(mtcars$qsec)
sp2 + scale_color_gradient2(midpoint = mid, low = "blue", mid = "white",
high = "red", space = "Lab" )

35 qsec 35 qsec 35 qsec

22.5 22.5 22.5
30 30 30

25 20.0 25 20.0 25 20.0

mpg

mpg

mpg

20 20 20
17.5 17.5 17.5
15 15 15

10 15.0 10 15.0 10 15.0

2 3 4 5 2 3 4 5 2 3 4 5
wt wt wt
26.3. GRADIENT OR CONTINUOUS COLORS 157

Note that, the functions scale_color_continuous() and

scale_fill_continuous() can be used also to set gradient colors.

26.3.2 Gradient between n colors

# Scatter plot
# Color points by the mpg variable
sp3 <- ggplot(mtcars, aes(x = wt, y = mpg)) +
geom_point(aes(color = mpg))
sp3

# Gradient between n colors

sp3 + scale_color_gradientn(colours = rainbow(5))

35 mpg 35 mpg
30 30 30 30
25 25
mpg

mpg

25 25
20 20
20 20
15 15
15 15
10 10
2 3 4 5 2 3 4 5
wt wt
Chapter 27

Point Shapes, colors and size

The different points shapes commonly used in R are illustrated in the figure below :

mtcars data is used in the following examples.

# Convert cyl as factor variable

mtcars$cyl <- as.factor(mtcars$cyl)

158
 159

Create a scatter plot and change point shapes, colors and size:

# Change shape, color and size

ggplot(mtcars, aes(x = wt, y = mpg)) +
geom_point(shape = 18, color = "steelblue", size = 4)

# change shape, color, fill, size

ggplot(mtcars, aes(x = wt, y = mpg)) +
geom_point(shape = 23, fill = "blue",
color = "darkred", size = 3)

# Change point shapes and colors by groups

ggplot(mtcars, aes(x = wt, y = mpg)) +
geom_point(aes(shape = cyl, color = cyl))

# Control the size by groups

# ggplot(mtcars, aes(x = wt, y = mpg)) +
# geom_point(aes(size = cyl))

35 35 35

30 30 30
cyl
25 25 25 4
mpg

mpg

mpg

20 20 20 6
8
15 15 15

10 10 10
2 3 4 5 2 3 4 5 2 3 4 5
wt wt wt

Note that, the argument fill can be used only for the point shapes 21 to 25.

Its also possible to manually change the appearance of points:

scale_shape_manual() : to change point shapes

scale_color_manual() : to change point colors
scale_size_manual() : to change the size of points
160 CHAPTER 27. POINT SHAPES, COLORS AND SIZE

# Change colors and shapes manually

ggplot(mtcars, aes(x=wt, y=mpg, group=cyl)) +
geom_point(aes(shape=cyl, color=cyl), size=2)+
scale_shape_manual(values=c(3, 16, 17))+
scale_color_manual(values=c('#999999','#E69F00', '#56B4E9'))+
theme(legend.position="top")

# Change the point size manually

ggplot(mtcars, aes(x=wt, y=mpg, group=cyl)) +
geom_point(aes(shape=cyl, color=cyl, size=cyl))+
scale_shape_manual(values=c(3, 16, 17))+
scale_color_manual(values=c('#999999','#E69F00', '#56B4E9'))+
scale_size_manual(values=c(1.5,2,3))+
theme(legend.position="top")

cyl 4 6 8 cyl 4 6 8

35 35

30 30

25 25
mpg

mpg

20 20

15 15

10 10
2 3 4 5 2 3 4 5
wt wt
Chapter 28

Line types

The different line types available in R software are : blank, solid, dashed,
dotted, dotdash, longdash, twodash.

Note that, line types can be also specified using numbers : 0, 1, 2, 3, 4, 5, 6. 0 is

for "blank", 1 is for "solid", 2 is for "dashed", ....

A graph of the different line types is shown below :

twodash

solid

longdash
Line types

dotted

dotdash

dashed

blank

1. Basic line plot

# Create some data

df <- data.frame(time=c("breakfeast", "Lunch", "Dinner"),
bill=c(10, 30, 15))
head(df)

161
162 CHAPTER 28. LINE TYPES

## time bill
## 1 breakfeast 10
## 2 Lunch 30
## 3 Dinner 15

# Basic line plot with points

# Change the line type
ggplot(data = df, aes(x = time, y = bill, group = 1)) +
geom_line(linetype = "dashed")+
geom_point()

30

25
bill

20

15

10
breakfeastDinner Lunch
time

2. Line plot with multiple groups

# Create some data

df2 <- data.frame(sex = rep(c("Female", "Male"), each=3),
time=c("breakfeast", "Lunch", "Dinner"),
bill=c(10, 30, 15, 13, 40, 17) )
head(df2)

## sex time bill

## 1 Female breakfeast 10
## 2 Female Lunch 30
## 3 Female Dinner 15
## 4 Male breakfeast 13
## 5 Male Lunch 40
## 6 Male Dinner 17
 163

# Line plot with multiple groups

# Change line types and colors by groups (sex)
ggplot(df2, aes(x=time, y=bill, group=sex)) +
geom_line(aes(linetype = sex, color = sex))+
geom_point(aes(color=sex))

40

30 sex
bill

Female
20 Male

10
breakfeastDinner Lunch
time
The functions below can be used to change the appearance of line types manually:

scale_linetype_manual() : to change line types

scale_color_manual() : to change line colors
scale_size_manual() : to change the size of lines

# Change line types, colors and sizes

ggplot(df2, aes(x=time, y=bill, group=sex)) +
geom_line(aes(linetype=sex, color=sex, size=sex))+
geom_point()+
scale_linetype_manual(values=c("twodash", "dotted"))+
scale_color_manual(values=c('#999999','#E69F00'))+
scale_size_manual(values=c(1, 1.5))

40

30 sex
bill

Female
20 Male

10
breakfeastDinner Lunch
time
Chapter 29

Axis limits: Minimum and

Maximum values

There are different functions for setting axis limits:

1. Without clipping (preferred):

p + coord_cartesian(xlim = c(5, 20), ylim = (0, 50)): Cartesian

coordinates. The Cartesian coordinate system is the most common type
of coordinate system. It will zoom the plot (like youre looking at it with
a magnifying glass), without clipping the data.

2. With clipping the data: (removes unseen data points): Observations not in
this range will be dropped completely and not passed to any other layers.

p + xlim(5, 20) + ylim(0, 50)

p + scale_x_continuous(limits = c(5, 20)) +
scale_y_continuous(limits = c(0, 50))

3. Expand the plot limits with data: This function is a thin wrapper around
geom_blank() that makes it easy to add data to a plot.

p + expand_limits(x = 0, y = 0): set the intercept of x and y axes at

(0,0)
p + expand_limits(x = c(5, 50), y = c(0, 150))

164
 165

We start by creating a plot using cars data set:

data(cars)
p <- ggplot(cars, aes(x = speed, y = dist)) + geom_point()

1. Use coord_cartesian(), xlim(), ylim() and expand_limits():

# Default plot
print(p)

# Change axis limits using coord_cartesian()

p + coord_cartesian(xlim =c(5, 20), ylim = c(0, 50))

125 50
100 40
75 30
dist

dist

50 20
25 10
0 0
5 10 15 20 25 5 10 15 20
speed speed

Note that, the function expand_limits() can be also used to quickly set the
intercept of x and y axes at (0,0).

# set the intercept of x and y axis at (0,0)

p + expand_limits(x = 0, y=0)

2. Use scale_x_x() functions: The functions scale_x_continuous() and

scale_y_continuous() can be used to change x and y axis limits/labels,
respectively:

# Change x and y axis labels, and limits

p + scale_x_continuous(name="Speed of cars", limits=c(0, 30)) +
scale_y_continuous(name="Stopping distance", limits=c(0, 150))
Chapter 30

Axis transformations: log and sqrt

1. Create a scatter plot:

data(cars)
p <- ggplot(cars, aes(x = speed, y = dist)) + geom_point()

2. Functions for continuous axis transformations:

p + scale_x_log10(), p + scale_y_log10() : Plot x and y on log10 scale,

respectively.

p + scale_x_sqrt(), p + scale_y_sqrt() : Plot x and y on square root

scale, respectively.

p + scale_x_reverse(), p + scale_y_reverse() : Reverse direction of axes

p + coord_trans(x ="log10", y="log10") : transformed cartesian coordinate

system. Possible values for x and y are "log2", "log10", "sqrt", ...

p + scale_x_continuous(trans=log2), p +
scale_y_continuous(trans=log2) : another allowed value for the
argument trans is log10

3. Use the function scale_xx_continuous() to transform axis scales:

166
 167

# Default scatter plot

print(p)

# Log transformation using scale_xx()

# possible values for trans : 'log2', 'log10','sqrt'
p + scale_x_continuous(trans='log2') +
scale_y_continuous(trans='log2')

# Format axis tick mark labels to show exponents

require(scales)
p + scale_y_continuous(trans = log2_trans(),
breaks = trans_breaks("log2", function(x) 2^x),
labels = trans_format("log2", math_format(2^.x)))

# Reverse coordinates
p + scale_y_reverse()

125 27 0
100 64 26 25
75 25 50
dist

dist

dist

50
16 24 dist 75
23
25 4 22 100
0 21 125
5 10 15 20 25 4 8 16 5 10 15 20 25 5 10 15 20 25
speed speed speed speed

4. Format axis tick mark labels: The scales package is required to access
break formatting functions.

require(scales)
# Percent
p + scale_y_continuous(labels = percent)

# Dollar
p + scale_y_continuous(labels = dollar)

# Scientific
p + scale_y_continuous(labels = scientific)
168 CHAPTER 30. AXIS TRANSFORMATIONS: LOG AND SQRT

12,500% $125 1.25e+02

10,000% $100 1.00e+02
7,500% $75 7.50e+01
dist

dist

dist
5,000% $50 5.00e+01
2,500% $25 2.50e+01
0% $0 0.00e+00
5 10 15 20 25 5 10 15 20 25 5 10 15 20 25
speed speed speed

5. Display log tick marks: the function annotation_logticks() will be used.

Note that, these tick marks make sense only for base 10.

Data: Animals data sets, from the package MASS.

# Required package
require(MASS) # to access Animals data sets
require(scales) # to access break formatting functions
data(Animals) # Load data

# x and y axis are transformed and formatted

p2 <- ggplot(Animals, aes(x = body, y = brain)) + geom_point() +
scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
theme_bw()

# log-log plot without log tick marks

p2

# Show log tick marks

p2 + annotation_logticks()
 169

103 103
brain

brain
102 102

101 101

100 100

100 102 104 100 102 104

body body

Note that, default log ticks are on bottom and left.

To specify the sides of the log ticks :

# Log ticks on left and right

p2 + annotation_logticks(sides="lr")

# All sides
p2+annotation_logticks(sides="trbl")

Allowed values for the argument sides are the combination of t(top), r(right),
b(bottom), l(left).
Chapter 31

Date Axes

The functions scale_x_date() and scale_y_date() are used to format date axes.
Create some time series data sets:

set.seed(1234)
df <- data.frame(
date = seq(Sys.Date(), len=100, by="1 day")[sample(100, 50)],
price = runif(50)
)
df <- df[order(df$date), ]
head(df)

## date price
## 7 2016-04-20 0.49396092
## 24 2016-04-23 0.78312110
## 1 2016-05-01 0.07377988
## 23 2016-05-02 0.01462726
## 19 2016-05-05 0.05164662
## 25 2016-05-06 0.08996133

31.1 Format axis tick mark labels: days, weeks,

months
The R package scales is required.

170
31.1. FORMAT AXIS TICK MARK LABELS: DAYS, WEEKS, MONTHS 171

# Default plot
p <- ggplot(data=df, aes(x = date, y=price)) + geom_line()
p

# Format axis tick mark labels

# Format : month/day
require(scales)
p + scale_x_date(labels = date_format("%m/%d")) +
theme(axis.text.x = element_text(angle=45))

# Format : Week
p + scale_x_date(labels = date_format("%W"))

# Months only
p + scale_x_date(breaks = date_breaks("months"),
labels = date_format("%b")) +
theme(axis.text.x = element_text(angle=45))

0.75 0.75 0.75

price

0.50
price

price
0.50 0.50
0.25
0.25 0.25
0.00
05 1
5

06 1
07 5
07 1
5
1
/0
/1
/0
/1
/0
/1
/0

0.00 0.00
05

06

08

maimai
01 15
jui 01
jui 15
jul 01
jul 15
ao 01 17 19 22 24 26 28 31
date date date

0.75
price

0.50

0.25

0.00

ai

l
ju

ju

ao
m

date
172 CHAPTER 31. DATE AXES

31.2 Date axis limits

US economic time series data sets are used :

# Plot with dates

data("economics")
p <- ggplot(data = economics, aes(x = date, y = psavert)) +
geom_line(color = "steelblue")
p

# Axis limits c(min, max)

min <- as.Date("2002-1-1")
max <- max(economics$date)
p + scale_x_date(limits = c(min, max))

15 15
psavert

psavert

10 10

5 5

1970 1980 1990 2000 2010 2002 2004 2006 2008 2010 2012 2014
date date
Chapter 32

Axis Ticks : Customize Tick

Marks and Labels, Reorder and
Select items

1. Functions for changing the style of axis tick mark labels:

element_text(face, color, size, angle): change text style -

element_blank(): Hide text

2. Create a box plot:

data("ToothGrowth")
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
p <- ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_boxplot()
# print(p)

3. Change the style and the orientation angle of axis tick labels

173
174 CHAPTER 32. AXIS TICKS : CUSTOMIZE TICK MARKS AND LABELS

# Change the style of axis tick labels

# face can be "plain", "italic", "bold" or "bold.italic"
p + theme(axis.text.x = element_text(face="bold", color="#993333",
size=12, angle=45),
axis.text.y = element_text(face="bold", color="blue",
size=12, angle=45))

# Remove axis ticks and tick mark labels

p + theme(
axis.text.x = element_blank(), # Remove x axis tick labels
axis.text.y = element_blank(), # Remove y axis tick labels
axis.ticks = element_blank()) # Remove ticks
30
len
20

len
10

5
1

2
0.

dose dose

4. Change axis lines: the function element_line() is used.

# Change the line type and color of axis lines

p + theme( axis.line = element_line(colour = "darkblue",
size = 1, linetype = "solid"))

30
len

20

10

0.5 1 2
dose
 175

5. Customize continuous and discrete axes

x or y axis can be discrete or continuous. In each of these two cases, the functions to
be used for setting axis ticks are different.

Discrete axes
scale_x_discrete(name, breaks, labels, limits): for X axis
scale_y_discrete(name, breaks, labels, limits): for y axis
Continuous axes
scale_x_continuous(name, breaks, labels, limits, trans): for X axis
scale_y_continuous(name, breaks, labels, limits, trans): for y axis

Briefly, the meaning of the arguments are as follow:

name : x or y axis labels

breaks : vector specifying which breaks to display

labels : labels of axis tick marks

limits : vector indicating the data range

scale_xx() functions can be used to change the following x or y axis parameters :

axis titles
axis limits (data range to display)
choose where tick marks appear
manually label tick marks

5.1. Discrete axes

Note that, in the examples below, well use only the functions scale_x_discrete()
and xlim() to customize x axis tick marks. The same kind of examples can be
applied to a discrete y axis using the functions scale_y_discrete() and ylim().
176 CHAPTER 32. AXIS TICKS : CUSTOMIZE TICK MARKS AND LABELS

# Default plot
print(p)

# Change x axis label and the order of items

p + scale_x_discrete(name ="Dose (mg)",
limits=c("2","1","0.5"))

# Change tick mark labels

p + scale_x_discrete(breaks=c("0.5","1","2"),
labels=c("D0.5", "D1", "D2"))

# Choose which items to display

p + scale_x_discrete(limits=c("0.5", "2"))

# or use this:
# p + xlim("0.5", "2") # same as above

30 30 30 30
len

20
len

len

len
20 20 20

10 10 10 10

0.5 1 2 2 1 0.5 D0.5 D1 D2 0.5 2

dose Dose (mg) dose dose
5.2 Continuous axes

# Default scatter plot

sp <- ggplot(cars, aes(x = speed, y = dist)) + geom_point()
sp

# Change x and y axis labels, and limits

sp + scale_x_continuous(name="Speed of cars", limits=c(0, 30)) +
scale_y_continuous(name="Stopping distance", limits=c(0, 150))

# Set tick marks on y axis: a tick mark is shown on every 50

sp + scale_y_continuous(breaks=seq(0, 150, 50))
 177

# Tick marks can be spaced randomly

sp + scale_y_continuous(breaks=c(0, 50, 65, 75, 150))

# Remove tick mark labels and gridlines

sp + scale_y_continuous(breaks=NULL)

# Format the labels

# +++++++++++++++++
require(scales)
# Possible values for labels = percent, scientific, ..
sp + scale_y_continuous(labels = percent) # labels as percents

125
Stopping distance

150
100 100
75 100 75
dist

dist

dist
65
50 50 50
50
25
0 0 0 0
5 10 15 20 25 0 10 20 30 5 10 15 20 25 5 10 15 20 25
speed Speed of cars speed speed
12,500%
10,000%
7,500%
dist

dist

5,000%
2,500%
0%
5 10 15 20 25 5 10 15 20 25
speed speed

Possible values for labels are comma, percent, dollar and scientific. For more examples,
read the documentation of the function trans_new() in scales package
Chapter 33

Themes and Background Colors

This chapter describes how to change the look of a plot theme (background color,
panel background color and grid lines). Youll also learn how to use ggplot2 base
themes to create your own theme.
ToothGrowth data will be used :

data("ToothGrowth")
# Convert the column dose from numeric to factor variable
ToothGrowth$dose <- as.factor(ToothGrowth$dose)

We start by creating a simple box plot:

p <- ggplot(ToothGrowth, aes(x=dose, y=len)) +

geom_boxplot()

33.1 Change plot themes: Quick functions

Several functions are available in ggplot2 package for changing quickly the theme of
plots :

theme_gray(): gray background color and white grid lines

theme_bw(): white background and gray grid lines

178
33.1. CHANGE PLOT THEMES: QUICK FUNCTIONS 179

theme_linedraw(): black lines around the plot

theme_light(): light gray lines and axis (more attention towards the data)

p + theme_gray(base_size = 14)

p + theme_bw()

p + theme_linedraw()

p + theme_light()

theme_gray theme_bw theme_linedraw theme_light

30 30 30 30
len

20
len

len

len
20 20 20

10 10 10 10

0.5 1 2 0.5 1 2 0.5 1 2 0.5 1 2

dose dose dose dose

theme_minimal(): no background annotations

theme_classic(): theme with axis lines and no grid lines (standard plot)

theme_void(): Empty theme, useful for plots with non-standard coordinates or for
drawings

theme_dark(): Dark background designed to make colours pop out

p + theme_minimal()

p + theme_minimal()

p + theme_void()

p + theme_dark()
180 CHAPTER 33. THEMES AND BACKGROUND COLORS

theme_void
theme_minimal theme_classic theme_dark
30
30 30 30
len

len
20 20 len20

len
20
10 10
10 10

0.5 1 2 0.5 1 2 0.5 1 2

0.5 1 2
dose dose dose dose

The functions theme_xx() can take the two arguments below :

base_size : base font size (to change the size of all plot text elements)

base_family : base font family

The size of all the plot text elements can be easily changed at once :

# Example 1
p + theme_gray(base_size = 10)

# Example 2
p + theme_gray(base_size = 20)

30
30
len

20
len

20

10
10

0.5 1 2
0.5 1 2
dose dose
Note that, the function theme_set() can be used to change the theme for the entire
session.
33.2. CUSTOMIZE PLOT BACKGROUND 181

theme_set(theme_gray(base_size = 20))

33.2 Customize plot background

The function theme() is used to control non-data parts of the graph including :

Line elements: axis lines, minor and major grid lines, plot panel border, axis
ticks background color, etc.

Text elements: plot title, axis titles, legend title and text, axis tick mark
labels, etc.

Rectangle elements: plot background, panel background, legend background,

etc.

There is a specific function to modify each of these three elements :

element_line() to modify the line elements of the theme

element_text() to modify the text elements

element_rect() to change the appearance of the rectangle elements

Note that, each of the theme elements can be removed using the function ele-
ment_blank()

33.2.1 Change colors

In this section well change the color of the plot panel background and the grid lines.

The functions theme() and element_rect(fill, colour, size, linetype) are

used for changing the plot panel background color.

The appearance of grid lines can be changed using the function ele-
ment_line(colour, size, linetype).
182 CHAPTER 33. THEMES AND BACKGROUND COLORS

# Change the colors of plot panel background to lightblue

# and the color of major/grid lines to white
p + theme(
panel.background = element_rect(fill = "#BFD5E3", colour = "#6D9EC1",
size = 2, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "white"),
panel.grid.minor = element_line(size = 0.25, linetype = 'solid',
colour = "white")
)

# Change the plot background color

p + theme(plot.background = element_rect(fill = "#BFD5E3"))

30
30
len

20
len

20

10
10

0.5 1 2
0.5 1 2
dose
dose

33.2.2 Remove panel borders and grid lines

It is possible to hide plot panel borders and grid lines with the function ele-
ment_blank() as follow :

# Hide panel borders and grid lines

# But change axis line
p + theme(panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(size = 0.5, linetype = "solid",
colour = "black"))
33.3. USE GGTHEMES 183

30
len

20

10

0.5 1 2
dose

33.3 Use ggthemes

You can change the entire appearance of a plot by using a custom theme. Jeffrey
Arnold has implemented the library ggthemes containing several custom themes.
Read more about ggthemes: https://github.com/jrnold/ggthemes
To use these themes install and load ggthemes package as follow :

install.packages("ggthemes") # Install
library(ggthemes) # Load

ggthemes package provides many custom themes and scales. Two of themes are
shown below:

p <- ggplot(ToothGrowth, aes(x = dose, y = len)) +

geom_boxplot(aes(fill = dose))
# theme_economist
p + theme_economist() + scale_fill_economist()

# theme_stata
p + theme_stata() + scale_fill_stata()
184 CHAPTER 33. THEMES AND BACKGROUND COLORS

30
dose 0.5 1 2

20
len
10
30
len

20
10 0.5 1 2
dose
0.5 1 2
dose dose 0.5 1 2

33.4 Create your theme

1. You can change the theme for the current R session using the function
theme_set() as follow :

theme_set(theme_gray(base_size = 20))

2. You can extract and modify the R code of theme_gray :

theme_gray

function (base_size = 11, base_family = "") {

half_line <- base_size/2
theme(
...
axis.text = element_text(size = rel(0.8), colour = "grey30"),
...
)
}

Note that, the function rel() modifies the size relative to the base size.
Chapter 34

Text Annotations

This article describes how to add a text annotation to a plot generated using ggplot2
package.
The functions below can be used :

geom_text(): adds text directly to the plot

geom_label(): draws a rectangle underneath the text, making it easier to read.
annotate(): useful for adding small text annotations at a particular location
on the plot
annotation_custom(): Adds static annotations that are the same in every
panel

Its also possible to use the R package ggrepel, which is an extension and provides
geom for ggplot2 to repel overlapping text labels away from each other.

Well start by describing how to use ggplot2 official functions for adding text annota-
tions. In the last sections, examples using ggrepel extensions are provided.

A subset of mtcars data is used:

set.seed(1234)
df <- mtcars[sample(1:nrow(mtcars), 10), ]
df$cyl <- as.factor(df$cyl)

185
186 CHAPTER 34. TEXT ANNOTATIONS

34.1 Text annotations using geom_text and

geom_label

# Simple scatter plot

sp <- ggplot(df, aes(wt, mpg, label = rownames(df)))+
geom_point()

# Add text, change colors by groups

# Change vertical justification
sp + geom_text(aes(label = rownames(df), color = cyl),
size = 3, vjust = -1)

# Add text at a particular coordinate

sp + geom_text(x = 3, y = 30, label = "Scatter plot",
color="red", fontface = 2)

Toyota
35 FiatCorolla 35
128
Honda Civic
30 30 Scatter plot
cyl
25 a 4 25
mpg

mpg

HornetRX4
Mazda 4 Drive
Ferrari DinoFirebird
Pontiac a 6
20 Valiant 20
Merc 450SE
a 8
15 15
Lincoln Continental
10 10
2 3 4 5 2 3 4 5
wt wt

geom_label() works like geom_text() but draws a rounded rectangle underneath

each label. This is useful when you want to label plots that are dense with data.

sp + geom_label()
34.2. ANNOTATION_CUSTOM : ADD A STATIC TEXT ANNOTATION 187

Others useful arguments for geom_text() and geom_label() are:

nudge_x and nudge_y: let you offset labels from their corresponding points.
The function position_nudge() can be also used.

check_overlap = TRUE: for avoiding overplotting of labels

hjust and vjust can now be character vectors (ggplot2 v >= 2.0.0): "left",
"center", "right", "bottom", "middle", "top". New options include "inward"
and "outward" which align text towards and away from the center of the plot
respectively.

fontface: Change fontface. Allowed values : 1 (normal), 2 (bold), 3 (italic)

and 4 (bold.italic).

34.2 annotation_custom : Add a static text anno-

tation
The functions annotation_custom() and textGrob() are used to add static anno-
tations which are the same in every panel.The grid package is required :

# Create a scatter plot

sp2 <- ggplot(mtcars, aes(x=wt, y=mpg, label=rownames(mtcars)))+
geom_point()

# Create a static text annotation

library(grid)
grob <- grobTree(textGrob("Scatter plot", x=0.1, y=0.95, hjust=0,
gp=gpar(col="red", fontsize=13, fontface="italic")))
# Plot
sp2 + annotation_custom(grob) +
facet_wrap(~cyl, scales="free")
188 CHAPTER 34. TEXT ANNOTATIONS

4 6 8
Scatter plot Scatter plot Scatter plot
21
17.5
30
20
mpg

15.0

25 19
12.5
18
10.0
1.5 2.0 2.5 3.0 2.75 3.00 3.25 3.50 3.5 4.0 4.5 5.0 5.5
wt

Case of facet (Chapter 37): the annotation is at the same place (in each facet) even
if the axis scales vary.

34.3 ggrepel: Avoid overlapping of text labels

Install ggrepel package as follow:

install.packages("ggrepel")

There are two important functions in ggrepel R packages:

geom_label_repel()
geom_text_repel()

We start by creating a simple scatter plot using a subset of the mtcars data set
containing 15 rows.

1. Prepare some data:

# Take a subset of 15 random points

set.seed(1234)
ss <- sample(1:32, 15)
df <- mtcars[ss, ]
34.3. GGREPEL: AVOID OVERLAPPING OF TEXT LABELS 189

2. Create a scatter plot:

p <- ggplot(df, aes(wt, mpg)) +

geom_point(color = 'red') +
theme_minimal(base_size = 10)

3. Add text labels:

# Add text annotations using ggplot2::geom_text

p + geom_text(aes(label = rownames(df)),
size = 3.5)

35
Toyota Corolla
Fiat 128
30 Lotus
Honda
Europa
Civic

25
Porsche 914-2
mpg

Hornet 4 Drive
Mazda RX4
20 Ferrari Dino Pontiac Firebird
Valiant
Merc 450SE
15 AMC Javelin
Maserati Bora
Camaro Z28
10 Lincoln Continental

2 3 4 5
wt

# Use ggrepel::geom_text_repel
require("ggrepel")
set.seed(42)
p + geom_text_repel(aes(label = rownames(df)),
size = 3.5)
190 CHAPTER 34. TEXT ANNOTATIONS

35
Fiat 128
Toyota Corolla
30 Honda Civic
Lotus EuropaPorsche 914-2
25
Mazda RX4 Hornet 4 Drive
mpg

20 Pontiac Firebird
Valiant
Ferrari Dino Merc 450SE
AMC Javelin
15
Maserati Bora
Lincoln Continental
10 Camaro Z28

2 3 4 5
wt

# Use ggrepel::geom_label_repel and

# Change color by groups
set.seed(42)
p + geom_label_repel(aes(label = rownames(df),
fill = factor(cyl)), color = 'white',
size = 3.5) +
theme(legend.position = "bottom")

35
Toyota Corolla Fiat 128
30
Honda Civic
Lotus Europa
25 Hornet 4 Drive
mpg

Porsche 914-2 Pontiac Firebird

20 Mazda RX4 Valiant Merc 450SE
15 Ferrari Dino Maserati Bora
AMC Javelin Camaro Lincoln
Z28 Continental
10

2 3 4 5
wt

factor(cyl) a 4 a 6 a 8
Chapter 35

Add Straight Lines to a Plot:

Horizontal, Vertical and
Regression Lines

The R function below can be used :

geom_hline(yintercept, linetype, color, size): for horizontal lines

geom_vline(xintercept, linetype, color, size): for vertical lines
geom_abline(intercept, slope, linetype, color, size): for regression lines
geom_segment() to add segments

1. Creating a simple scatter plot

# Simple scatter plot

sp <- ggplot(data = mtcars, aes(x = wt, y = mpg)) + geom_point()

2. Add straight lines and segments

# Add horizontal line at y = 2O; change line type and color

sp + geom_hline(yintercept=20, linetype="dashed", color = "red")

# Add vertical line at x = 3; change line type, color and size

191
192 CHAPTER 35. ADD STRAIGHT LINES TO A PLOT

sp + geom_vline(xintercept = 3, color = "blue", size=1.5)

# Add regression line

sp + geom_abline(intercept = 37, slope = -5, color="blue")+
ggtitle("y = -5X + 37")

# Add a vertical line segment

sp + geom_segment(aes(x = 4, y = 15, xend = 4, yend = 27))

# Add horizontal line segment

sp + geom_segment(aes(x = 2, y = 15, xend = 3, yend = 15))

# Add arrow at the end of the segment

require(grid)
sp + geom_segment(aes(x = 5, y = 30, xend = 3.5, yend = 25),
arrow = arrow(length = unit(0.5, "cm")))

35 35
y = -5X + 37
35
30 30
30
25 25
mpg

mpg

25
mpg

20 20
20
15 15 15

10 10 10
2 3 4 5 2 3 4 5 2 3 4 5
wt wt wt
35 35 35

30 30 30

25 25 25
mpg

mpg

mpg

20 20 20

15 15 15

10 10 10
2 3 4 5 2 3 4 5 2 3 4 5
wt wt wt
Chapter 36

Rotate a Plot: Flip and Reverse

To rotate a plot, the function below can be used:

coord_flip(): Create horizontal plots

scale_x_reverse(), scale_y_reverse(): Reverse the axes

set.seed(1234)
# Basic histogram
hp <- qplot(x=rnorm(200), geom="histogram")
hp
# Horizontal histogram
hp + coord_flip()
# Y axis reversed
hp + scale_y_reverse()

3 0
20 2
rnorm(200)

5
15 1
count

count

0 10
10
-1
5 15
-2
0 -3
-2 0 2 0 5 10 15 20 -3 -2 -1 0 1 2
rnorm(200) count rnorm(200)

193
Chapter 37

Facets: Split a Plot into a Matrix

of Panels

Facets divide a plot into subplots based on the values of one or more categorical
variables. There are two main functions for faceting :

facet_grid()
facet_wrap()

Create a box plot filled by groups:

# Load data and convert dose to a factor variable

data("ToothGrowth")
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
# Box plot
p <- ggplot(ToothGrowth, aes(x=dose, y=len, group=dose)) +
geom_boxplot(aes(fill=dose))
p

194
 195

30
dose
0.5
len

20
1
2
10

0.5 1 2
dose
The following functions can be used for facets:

p + facet_grid(supp ~.): Facet in vertical direction based on the levels of supp

variable.
p + facet_grid(.~supp): Facet in horizontal direction based on the levels of supp
variable.
p + facet_grid(dose ~supp) Facet in horizontal and vertical directions based on
two variables: dose and supp.
p + facet_wrap(~fl) Place facet side by side into a rectangular layout

1. Facet with one discrete variable: Split by the levels of the group supp

# Split in vertical direction

p + facet_grid(supp ~ .)

# Split in horizontal direction

p + facet_grid(. ~ supp)

30 OJ VC
OJ

20 dose
30 dose
10 0.5
len

0.5
len

1 20
30 1
2
VC

20
10 2
10

0.5 1 2 0.5 1 2 0.5 1 2

dose dose
196 CHAPTER 37. FACETS: SPLIT A PLOT INTO A MATRIX OF PANELS

2. Facet with two discrete variables: Split by the levels of the groups dose
and supp

# Facet by two variables: dose and supp.

# Rows are dose and columns are supp
p + facet_grid(dose ~ supp)

# Facet by two variables: reverse the order of the 2 variables

# Rows are supp and columns are dose
p + facet_grid(supp ~ dose)

OJ VC 0.5 1 2
30 30
0.5

20

OJ
10 20
dose dose
30 0.5 10 0.5
len

len

20
1

10 1 1
30
2 VC 2
30 20
20
2

10
10
0.5 1 2 0.5 1 2 0.51 2 0.51 2 0.51 2
dose dose

Note that, you can use the argument margins to add additional facets which contain
all the data for each of the possible values of the faceting variables

p + facet_grid(dose ~ supp, margins=TRUE)

3. Facet scales

By default, all the panels have the same scales (scales=fixed). They can be made
independent, by setting scales to free, free_x, or free_y.

p + facet_grid(dose ~ supp, scales='free')

 197

4. Facet labels: The argument labeller can be used to control the labels of the
panels.

p + facet_grid(dose ~ supp, labeller=label_both)

supp: OJ supp: VC

dose: 0.5
30
20
10
dose
30 0.5
dose: 1
len

20
1
10
2
30
dose: 2

20
10
0.5 1 2 0.5 1 2
dose
The appearance of facet labels can be modified as follow :

# Change facet text font. Possible values for the font style:
#'plain', 'italic', 'bold', 'bold.italic'.
p + facet_grid(dose ~ supp)+
theme(strip.text.x = element_text(size=12, color="red",
face="bold.italic"),
strip.text.y = element_text(size=12, color="red",
face="bold.italic"))

# Change the apperance of the rectangle around facet label

p + facet_grid(dose ~ supp)+
theme(strip.background = element_rect(colour="black", fill="white",
size=1.5, linetype="solid"))
198 CHAPTER 37. FACETS: SPLIT A PLOT INTO A MATRIX OF PANELS

OJ VC OJ VC

30 30

0.5

0.5
20 20
10 10
dose dose
30 0.5 30 0.5

len
len

20 20

1
1
1 1
10 10
2 2
30 30
20 20
2

2
10 10

0.5 1 2 0.5 1 2 0.5 1 2 0.5 1 2

dose dose

5. facet_wrap: Facets can be placed side by side using the function

facet_wrap() as follow :

bp + facet_wrap(~ dose)

bp + facet_wrap(~ dose, ncol=2)

0.5 1 2 0.5 1
30
30 20
dose dose
10
0.5 0.5
len

len

20
1 2 1
30
2 2
10 20
10
0.5 1 2 0.5 1 2 0.5 1 2 0.5 1 2
dose dose
Chapter 38

Position Adjustements

Position adjustments determine how to arrange geoms. The argument position is

used to adjust geom positions:

p <- ggplot(mpg, aes(fl, fill = drv))

# Arrange elements side by side

p + geom_bar(position = "dodge")

# Stack objects on top of one another,

# and normalize to have equal height
p + geom_bar(position = "fill")

1.00

60 drv drv
0.75
4 4
count

count

40 0.50
f f
20 r 0.25 r

0 0.00
c d e p r c d e p r
fl fl

# Stack elements on top of one another

p + geom_bar(position = "stack")

199
200 CHAPTER 38. POSITION ADJUSTEMENTS

# Add random noise to X and Y position

# of each element to avoid overplotting
ggplot(mpg, aes(cty, hwy)) +
geom_point(position = "jitter")

150 40
drv
4
count

hwy
100 30
f
50 20
r

0
c d e p r 10 20 30
fl cty

Note that, each of these position adjustments can be done using a function with
manual width and height argument.

position_dodge(width, height)
position_fill(width, height)
position_stack(width, height)
position_jitter(width, height)

p + geom_bar(position = position_dodge(width = 1))

60 drv
4
count

40
f
20 r

0
c d e p r
fl

See bar plots chapter: Chapter 20

Chapter 39

Coordinate Systems

p <- ggplot(mpg, aes(fl)) + geom_bar()

The coordinate systems in ggplot2 are:

p + coord_cartesian(xlim = NULL, ylim = NULL): Cartesian coordinate

system (default). Its the most familiar and common, type of coordinate system.

p + coord_fixed(ratio = 1, xlim = NULL, ylim = NULL): Cartesian co-

ordinates with fixed relationship between x and y scales. The ratio
represents the number of units on the y-axis equivalent to one unit on the x-axis.
The default, ratio = 1, ensures that one unit on the x-axis is the same length as
one unit on the y-axis.

p + coord_flip(. . . ): Flipped cartesian coordinates. Useful for creating

horizontal plot by rotating.

p + coord_polar(theta = x, start = 0, direction = 1): Polar coordinates.

The polar coordinate system is most commonly used for pie charts, which are a
stacked bar chart in polar coordinates.

p + coord_trans(x, y, limx, limy): Transformed cartesian coordinate

system.

coord_map(): Map projections. Provides the full range of map projections

available in the mapproj package.

201
202 CHAPTER 39. COORDINATE SYSTEMS

1. Arguments for coord_cartesian(), coord_fixed() and coord_flip()

xlim, ylim: limits for the x and y axis, respectively
ratio: aspect ratio, expressed as y/x
. . . : Other arguments passed onto coord_cartesian
2. Arguments for coord_polar()
theta: variable to map angle to (x or y)
start: offset of starting point from 12 oclock in radians
direction: 1, clockwise; -1, anticlockwise
3. Arguments for coord_trans()
x, y: transformers for x and y axes
limx, limy: limits for x and y axes.

p + coord_cartesian(ylim = c(0, 200)) # change y limits

p + coord_fixed(ratio = 1/50) # change ratio
p + coord_flip() # flip the plot

200
r
150 p
count

100 150 e
fl
count

100
50 d
50
c
0 0
c d e p r c d e p r 0 50 100 150
fl fl count

p + coord_polar(theta = "x", direction = 1)

p + coord_trans(y = "sqrt")

160
120
160 r c 80
count

120
80 40
count

40
0
p d
0
e c d e p r
fl fl
 Part VI

Extensions to ggplot2

203
Chapter 40

Arrange Multiple Graphs on the

Same Page

To arrange multiple ggplot2 graphs on the same page, the standard R functions - par()
and layout() - cannot be used.

This chapter will show you, step by step, how to put several ggplots on a single page.

Key functions:

grid.arrange()[in the package gridExtra]

plot_grid() and draw_plot() [in the package cowplot]

40.1 Required R packages

The R packages gridExtra and cowplot are required.

1. Installation:

install.packages("gridExtra")
install.packages("cowplot")

204
40.2. DATA 205

2. Loading:

library("gridExtra")
library("cowplot")

40.2 Data
ToothGrowth and economics data sets are used :

# Load ToothGrowth
# Convert the variable dose from a numeric to a factor variable
data("ToothGrowth")
ToothGrowth$dose <- as.factor(ToothGrowth$dose)

data("economics") # Load economics

data("diamonds") # Load diamonds

40.3 cowplot: Arrange publication-ready plots

The cowplot package, developed by Claus O. Wilke provides a publication-ready
theme for ggplot2 and allows to combine multiple plots in the same figure. Well start
by creating some plots, which will be combined using specific functions provided by
the cowplot package.

40.3.1 Create some plots

Well create series of 3 different plots:

Box plot and dot plot using the ToothGrowth data set
Line plot using the economics data set

Well use custom colors to manually change line and fill colors (functions:
scale_color_manual() and scale_fill_manual(); see Chapter 26)
206 CHAPTER 40. ARRANGE MULTIPLE GRAPHS ON THE SAME PAGE

Define a custom set of 3 colors:

# A set of 3 colors
my3cols <- c("#E7B800", "#2E9FDF", "#FC4E07")

Create a box plot and a dot plot:

require(cowplot)

p <- ggplot(ToothGrowth, aes(x = dose, y = len))

# Box plot (bp)

bxp <- p + geom_boxplot(aes(color = dose)) +
scale_color_manual(values = my3cols)
bxp

# Dot plot (dp)

dp <- p + geom_dotplot(aes(color = dose, fill = dose),
binaxis='y', stackdir='center') +
scale_color_manual(values = my3cols) +
scale_fill_manual(values = my3cols)
dp

30 30
dose dose
0.5 0.5
len

len

20 20
1 1
2 2
10 10

0.5 1 2 0.5 1 2
dose dose

Create a line plot:

40.3. COWPLOT: ARRANGE PUBLICATION-READY PLOTS 207

lp <- ggplot(economics, aes(x = date, y = psavert)) +

geom_line(color = "#E46726")
lp

15
psavert

10

1970 1980 1990 2000 2010

date

Note that the default design of cowplot has white background with no grid at all.
It looks similar to ggplot2s theme_classic(), but there are some subtle differences
with respect to font sizes. In many cases, this is the cleanest and most elegant way
to display the data.

If you want to add gridlines or to use the default ggplot2 theme, follow the R code
below:

# Add gridlines
bxp + background_grid(major = "xy", minor = "none")

# Use theme_gray()
bxp + theme_gray()

30 dose 30 dose
0.5 0.5
len

len

20 20
1 1

10 2 10 2

0.5 1 2 0.5 1 2
dose dose

The function background_grid() is from cowplot package.

208 CHAPTER 40. ARRANGE MULTIPLE GRAPHS ON THE SAME PAGE

40.3.2 Combine multiple plots

In this section well see how to combine the different plots created in the previous
section.

Key functions:

plot_grid(): Combines easily multiple plots

ggdraw() + draw_plot() + draw_plot_label(): Place graphs at partic-

ular locations with a particular sizes.

In the R code below, the function plot_grid() is used to combine a box plot (bxp),
a dot plot (dp) and a line plot (lp) on a grid of 2 columns and 2 rows:

plot_grid(bxp, dp, lp, labels = c("A", "B", "C"),

ncol = 2, nrow = 2)

A B
30 dose 30 dose
0.5 0.5
len

len

20 20
1 1
10 2 10 2

0.5 1 2 0.5 1 2
dose dose

C
15
psavert

10

1970 1980 1990 2000 2010

date

The combination of the functions ggdraw(), draw_plot() and

draw_plot_label() can be used to place graphs and labels at particular
locations with a particular sizes.
40.3. COWPLOT: ARRANGE PUBLICATION-READY PLOTS 209

ggdraw(): Initialize an empty drawing canvas

draw_plot(): Places a plot somewhere onto the drawing canvas.

draw_plot_label(): Adds a plot label to the upper left corner of a graph. It can
handle vectors of labels with associated coordinates.

Format of the function draw_plot():

draw_plot(plot, x = 0, y = 0, width = 1, height = 1)

plot: the plot to place (ggplot2 or a gtable)

x, y: The x/y location of the lower left corner of the plot.
width, height: the width and the height of the plot

Format of the function draw_plot_label():

draw_plot_label(label, x = 0, y = 1, size = 16, ...)

label: a vector of labels to be drawn

x, y: Vector containing the x and y position of the labels, respectively.
size: Font size of the label to be drawn

Note that, by default, coordinates run from 0 to 1, and the point (0, 0) is in the
lower left corner of the canvas (see the figure below).
210 CHAPTER 40. ARRANGE MULTIPLE GRAPHS ON THE SAME PAGE

Combine multiple plot with particular locations and different sizes:

ggdraw() +
draw_plot(bxp, x = 0, y = .5, width = .5, height = .5) +
draw_plot(dp, x = .5, y = .5, width = .5, height = .5) +
draw_plot(lp, x = 0, y = 0, width = 1, height = 0.5) +
draw_plot_label(label = c("A", "B", "C"),
x = c(0, 0.5, 0), y = c(1, 1, 0.5), size = 15)

A B
30 30
dose dose
0.5 0.5
len

len
20 20
1 1
2 2
10 10

0.5 1 2 0.5 1 2
dose dose

C
15
psavert

10

1970 1980 1990 2000 2010

date

40.3.3 Save multi-figure plots

Recall that, the function ggsave()[in ggplot2 package] (Chapter ??) can be used to
save ggplots. However, when working with cowplot, the function save_plot() [in
cowplot package] is preferred.

The cowplot default theme works nicely in conjunction with the save_plot(). The
output pdfs are nicely formatted and scaled.
40.4. GRIDEXTRA PACKAGE 211

For example, if we want to save the box plot generated in the previous section, we
might use this code:

# use save_plot() instead of ggsave() when using cowplot

save_plot("mpg.pdf", bxp,
base_aspect_ratio = 1.3 # make room for figure legend

The function save_plot() is also an alternative to ggsave() with a better support

for multi-figure plots generated with cowplot. Furthermore, it can can be told about
the grid layout.

For example, if we want to save a 2-by-2 figure, we might use this code:

plot2by2 <- plot_grid(bxp, dp, lp, labels = c("A", "B", "C"),

ncol = 2, nrow = 2)

save_plot("plot2by2.pdf", plot2by2,
ncol = 2, # we're saving a grid plot of 2 columns
nrow = 2, # and 2 rows
# each individual subplot should have an aspect ratio of 1.3
base_aspect_ratio = 1.3
)

40.4 gridExtra package

40.4.1 grid.arrange(): Arrange multiple plots on a page

The function grid.arrange()[in the package gridExtra] is another solution for

mixing multiple graphs.

Well combine the following plots:

the box plot, the dot plot and the line plot created in the previous sections
a bar plot created using the diamonds data sets as follow
212 CHAPTER 40. ARRANGE MULTIPLE GRAPHS ON THE SAME PAGE

# Define a set of 5 colors

my5cols <- c("#6D9EC1", "#646567", "#A29B32", "#E46726", "#F3BF94")

# Create a bar plot

data("diamonds")
brp <- ggplot(diamonds, aes(x = clarity)) +
geom_bar(aes(fill = cut)) + scale_fill_manual(values = my5cols)

Use grid.arrange() to combine the plot in a grid of 2 rows and 2 columns:

require(gridExtra)
grid.arrange(bxp, dp, lp, brp, ncol = 2, nrow =2)

30 30
dose dose
0.5 0.5
len

len

20 20
1 1
2 2
10 10

0.5 1 2 0.5 1 2
dose dose

15 cut
10000 Fair
psavert

Good
count

10
Very Good
5000
Premium
5
Ideal
0
1970 1980 1990 2000 2010 I1SI2SI1VS2
VS1
VVS2
VVS1
IF
date clarity
40.4. GRIDEXTRA PACKAGE 213

40.4.2 grid.arrange() and arrangeGrob(): Change col-

umn/row span of a plot

The function arangeGrop() helps to change the row/column span of a plot.

For example, using the R code below:

The box plot (bxp) will live in the first column

The dot plot (dp) and the bar plot (brp) will live in the second column

grid.arrange(bxp, arrangeGrob(dp, brp), ncol = 2)

30

dose
30
0.5
20
len

1
2
10

dose
20 0.5 0.5 1 2
len

1 dose
2

cut
10000
Fair
Good
count

10
Very Good
5000
Premium
Ideal

0
0.5 1 2 I1SI2SI1VS2
VS1
VVS2
VVS1
IF
dose clarity
214 CHAPTER 40. ARRANGE MULTIPLE GRAPHS ON THE SAME PAGE

Its also possible to use the argument layout_matrix in grid.arrange() function.

In the R code below layout_matrix is a 2x2 matrix (2 columns and 2 rows). The
first row is all 1s, thats where the first plot lives, spanning the three columns; the
second row contains plots 2, 3, 4, each occupying one row.

grid.arrange(brp, bxp, dp, ncol = 2, nrow = 2,

layout_matrix = rbind(c(1,1), c(2,3)))

cut
10000 Fair
Good
count

Very Good
5000
Premium
Ideal
0
I1 SI2 SI1 VS2 VS1 VVS2 VVS1 IF
clarity

30 30
dose dose
0.5 0.5
len

len

20 20
1 1
2 2
10 10

0.5 1 2 0.5 1 2
dose dose

40.4.3 Use common legend for multiple graphs

This can be done in four simple steps :

1. Create the plots : p1, p2, . . . .

2. Save the legend of the plot p1 as an external graphical element (called a grob
in Grid terminology)
40.4. GRIDEXTRA PACKAGE 215

3. Remove the legends from all plots

4. Draw all the plots with only one legend in the right panel

To save the legend of a ggplot, the helper function below can be used :

# Get plot legend

get_legend <- function(myggplot){
require(gridExtra)
tmp <- ggplot_gtable(ggplot_build(myggplot))
leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
legend <- tmp$grobs[[leg]]
return(legend)
}

Well arrange the box plot (bxp) and the dot plot (dp) created in the previous sections.

# 2. Save the legend from the dot plot

legend <- get_legend(dp)

# 3. Remove the legend from the box plot and the dot plot
bxp2 <- bxp + theme(legend.position="none")
dp2 <- dp + theme(legend.position="none")

# 4. Arrange bxp2, dp and the legend with a specific width

grid.arrange(bxp2, dp2, legend, ncol = 3,
widths = c(2.3, 2.3, 0.8))

30 30

dose
len

len

20 20
0.5
1
10 10
2

0.5 1 2 0.5 1 2
dose dose
216 CHAPTER 40. ARRANGE MULTIPLE GRAPHS ON THE SAME PAGE

In the R code above, the argument widths is a vector containing 3 values specifying
the width of the box plot (bxp2), the dot plot (dp2) and the legend, respectively.

Its also possible to use the argument layout_matrix to customize legend position.
We start by creating a dot plot with a top legend position. Next, we save the legend
and remove it from the dot plot:

# 1. Dot plot with legend at the top

dp2 <- dp + theme(legend.position = "top")

# 2. Save the legend

legend <- get_legend(dp2)

# 3. Remove the legend from the dot plot

dp2 <- dp2 + theme(legend.position = "none")

In the R code below, layout_matrix is a 2X2 matrix:

The first row (height = 2.5) is where the first plot (bxp2) and the second plot
(dp) live
The second row (height = 0.2) is where the legend lives spanning 2 columns

Bottom-center legend:

grid.arrange(bxp2, dp2, legend, ncol=2, nrow = 2,

layout_matrix = rbind(c(1,2), c(3,3)),
widths = c(2.7, 2.7), heights = c(2.5, 0.2))

30 30
len

len

20 20

10 10

0.5 1 2 0.5 1 2
dose dose
dose 0.5 1 2
40.4. GRIDEXTRA PACKAGE 217

Top-center legend:

The legend (plot 1) lives in the first row (height = 0.2) spanning two columns
bxp2 (plot 2) and dp2 (plot 3) live in the second row (height = 2.5)

grid.arrange(legend, bxp2, dp2, ncol=2, nrow = 2,

layout_matrix = rbind(c(1,1), c(2,3)),
widths = c(2.7, 2.7), heights = c(0.2, 2.5))

dose 0.5 1 2

30 30
len

len

20 20

10 10

0.5 1 2 0.5 1 2
dose dose

40.4.4 Scatter plot with marginal density plots

Define a custom set of 3 colors:

# Another set of 3 colors

my3cols <- c("#6D9EC1", "#646567", "#A29B32")

Step 1/3. Create some data :

set.seed(1234)
x <- c(rnorm(350, mean = -1), rnorm(350, mean = 1.5),
rnorm(350, mean = 4))

y <- c(rnorm(350, mean = -0.5), rnorm(350, mean = 1.7),

rnorm(350, mean = 2.5))
218 CHAPTER 40. ARRANGE MULTIPLE GRAPHS ON THE SAME PAGE

group <- as.factor(rep(c(1, 2, 3), each = 350))

df2 <- data.frame(x, y, group)

head(df2)

## x y group
## 1 -2.20706575 -0.715413865 1
## 2 -0.72257076 -0.009793331 1
## 3 0.08444118 -0.440606576 1
## 4 -3.34569770 -0.441687947 1
## 5 -0.57087531 1.338363107 1
## 6 -0.49394411 -0.112349101 1

Step 2/3. Create the plots:

# Scatter plot of x and y variables and color by groups

scatterPlot <- ggplot(df2, aes(x, y)) +
geom_point(aes(color = group)) +
scale_color_manual(values = my3cols) +
theme(legend.position=c(0,1), legend.justification=c(0,1))

# Marginal density plot of x (top panel)

xdensity <- ggplot(df2, aes(x)) +
geom_density(aes(fill = group), alpha=.8) +
scale_fill_manual(values = my3cols) +
theme(legend.position = "none")

# Marginal density plot of y (right panel)

ydensity <- ggplot(df2, aes(y)) +
geom_density(aes(fill=group), alpha=.8) +
scale_fill_manual(values = my3cols) +
theme(legend.position = "none") + coord_flip()

Create a blank placeholder plot :

40.4. GRIDEXTRA PACKAGE 219

blankPlot <- ggplot()+geom_blank(aes(1,1))+ theme_void()

Step 3/3. Put the plots together:

Arrange ggplot2 with adapted height and width for each row and column :

require("gridExtra")
grid.arrange(xdensity, blankPlot, scatterPlot, ydensity,
ncol=2, nrow=2, widths=c(4, 1.4), heights=c(1.4, 4))

0.4
density

0.3
0.2
0.1
0.0
-2.5 0.0 2.5 5.0
x
6 6
group
4 1 4
2
3
2 2
y

0 0

-2 -2

-2.5 0.0 2.5 5.0 0.0

0.1
0.2
0.3
0.4
x density

40.4.5 Create a complex layout using the function viewport()

The different steps are :

1. Create plots : p1, p2, p3, . . . .

2. Move to a new page on a grid device using the function grid.newpage()
220 CHAPTER 40. ARRANGE MULTIPLE GRAPHS ON THE SAME PAGE

3. Create a layout 2X2 - number of columns = 2; number of rows = 2

4. Define a grid viewport : a rectangular region on a graphics device
5. Print a plot into the viewport

require(grid)
# Move to a new page
grid.newpage()

# Create layout : nrow = 2, ncol = 2

pushViewport(viewport(layout = grid.layout(2, 2)))

# A helper function to define a region on the layout

define_region <- function(row, col){
viewport(layout.pos.row = row, layout.pos.col = col)
}

# Arrange the plots

print(scatterPlot, vp=define_region(1, 1:2))
print(xdensity, vp = define_region(2, 1))
print(ydensity, vp = define_region(2, 2))
40.5. GGEXTRA: ADD MARGINAL DISTRIBUTIONS PLOTS 221

4
group
1
2
2
y

0 3

-2

-2.5 0.0 2.5 5.0

x
6
0.4
4
0.3
density

2
y

0.2
0
0.1
-2
0.0
-2.5 0.0 2.5 5.0 0.0 0.1 0.2 0.3 0.4
x density

40.5 ggExtra: Add marginal distributions plots

The package ggExtra (https://github.com/daattali/ggExtra) is an easy-to-use pack-
age developed by Dean Attali, for adding marginal histograms, boxplots or density
plots to ggplot2 scatter plots.
The package can be installed and used as follow:

# Install
install.packages("ggExtra")

library("ggExtra")

# Marginal density plot

ggMarginal(scatterPlot)
222 CHAPTER 40. ARRANGE MULTIPLE GRAPHS ON THE SAME PAGE

# Marginal histogram plot

ggMarginal(scatterPlot, type = "histogram",
fill = "#6D9EC1", color = "#BFD5E3")

6 6
group group
4 1 4 1
2 2
2 2
3 3
y

y
0 0

-2 -2

-2.5 0.0 2.5 5.0 -2.5 0.0 2.5 5.0

x x

40.6 Insert an external graphical element inside a

ggplot
The function annotation_custom() [in ggplot2] can be used for adding tables,
plots or other grid-based elements. The simplified format is :

annotation_custom(grob, xmin, xmax, ymin, ymax)

grob: the external graphical element to display

xmin, xmax : x location in data coordinates (horizontal location)
ymin, ymax : y location in data coordinates (vertical location)

The different steps are :

1. Create a scatter plot of y = f(x)

40.6. INSERT AN EXTERNAL GRAPHICAL ELEMENT INSIDE A GGPLOT223

2. Add, for example, the box plot of the variables x and y inside the scatter plot
using the function annotation_custom()

As the inset box plot overlaps with some points, a transparent background is used
for the box plots.

# Create a transparent theme object

transparent_theme <- theme(
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.text.x = element_blank(),
axis.text.y = element_blank(),
axis.ticks = element_blank(),
panel.grid = element_blank(),
axis.line = element_blank(),
panel.background = element_rect(fill = "transparent",colour = NA),
plot.background = element_rect(fill = "transparent",colour = NA))

Create the graphs :

p1 <- scatterPlot # see previous sections for the scatterPlot

# Box plot of the x variable

p2 <- ggplot(df2, aes(factor(1), x))+
geom_boxplot(width=0.3)+coord_flip()+
transparent_theme

# Box plot of the y variable

p3 <- ggplot(df2, aes(factor(1), y))+
geom_boxplot(width=0.3)+
transparent_theme

# Create the external graphical elements

# called a "grop" in Grid terminology
p2_grob = ggplotGrob(p2)
p3_grob = ggplotGrob(p3)
224 CHAPTER 40. ARRANGE MULTIPLE GRAPHS ON THE SAME PAGE

# Insert p2_grob inside the scatter plot

xmin <- min(x); xmax <- max(x)
ymin <- min(y); ymax <- max(y)
p1 + annotation_custom(grob = p2_grob, xmin = xmin, xmax = xmax,
ymin = ymin-1.5, ymax = ymin+1.5)

6
group
1
4
2
3
2
y

-2

-2.5 0.0 2.5 5.0

x

# Insert p3_grob inside the scatter plot

p1 + annotation_custom(grob = p3_grob,
xmin = xmin-1.5, xmax = xmin+1.5,
ymin = ymin, ymax = ymax)
40.7. MIX TABLE, TEXT AND GGPLOT2 GRAPHS 225

6
group
1
4
2
3
2
y

-2

-2.5 0.0 2.5 5.0

x

40.7 Mix table, text and ggplot2 graphs

The functions below are required :

tableGrob() [in the package gridExtra] : for adding a data table to a graphic
device
splitTextGrob() [in the package RGraphics] : for adding a text to a graph

Make sure that the package RGraphics is installed.

library(RGraphics)
library(gridExtra)

# Table
p1 <- tableGrob(head(ToothGrowth, 3))

# Text
text <- paste0("ToothGrowth data describes the effect ",
"of Vitamin C on tooth growth in Guinea pigs.")
p2 <- splitTextGrob(text)
226 CHAPTER 40. ARRANGE MULTIPLE GRAPHS ON THE SAME PAGE

# Box plot
p3 <- ggplot(ToothGrowth, aes(x = dose, y = len)) +
geom_boxplot(aes(color = dose)) +
scale_color_manual(values = my3cols)

# Arrange the plots on the same page

grid.arrange(p1, p2, p3, ncol=1,
heights = c(0.25, 0.2, 0.55))

len supp dose

1 4.2 VC 0.5
2 11.5 VC 0.5
3 7.3 VC 0.5
ToothGrowth data describes the effect of Vitamin C
on tooth growth in Guinea pigs.

30
dose
0.5
len

20
1
2
10

0.5 1 2
dose
Chapter 41

Correlation Matrix Visualization

The R packages GGally and ggcorrplot are two extensions to ggplot2 for displaying
a correlation matrix.
Compared to GGally, the ggcorrplot package provides many options for visualizing
a correlation matrix. For example, it provides a solution for reordering the correlation
matrix and displays the significance level on the correlogram. It includes also a
function for computing a matrix of correlation p-values.

41.1 GGally
Compute and visualize a correlation matrix:

# Correlation matrix
library("GGally")
mydata <- mtcars[, c(1,3,4,5,6,7)]
ggcorr(mydata, palette = "RdBu", label = TRUE)

227
228 CHAPTER 41. CORRELATION MATRIX VISUALIZATION

qsec

rho
wt -0.2
(-1,-0.75]
(-0.75,-0.5]
drat -0.7 0.1 (-0.5,-0.25]
(-0.25,0]
(0,0.25]
hp -0.4 0.7 -0.7
(0.25,0.5]
(0.5,0.75]
disp 0.8 -0.7 0.9 -0.4 (0.75,1]

mpg -0.8 -0.8 0.7 -0.9 0.4

# Matrix of scatter plot

ggpairs(mydata)

30 Corr: Corr: Corr: Corr: Corr:

mpg

25
20 -0.848 -0.776 0.681 -0.868 0.419
15
400 Corr: Corr: Corr: Corr:
disp

300
200 0.791 -0.71 0.888 -0.434
100
300
Corr: Corr: Corr:
hp

200
100 -0.449 0.659 -0.708
5.0
4.5 Corr: Corr:
drat

4.0
3.5 -0.712 0.0912
3.0
5
4 Corr:
wt

3
2
-0.175
22
qsec

20
18
16
101520253035
mpg 100200 300400 100 hp
disp 200 300 3.03.54.04.55.0 2 3wt4 5
drat 16qsec
18 20 22
41.2. GGCORRPLOT 229

41.2 ggcorrplot

41.2.1 Installation and loading

ggcorrplot can be installed from CRAN as follow:

install.packages("ggcorrplot")

Or, install the latest version from GitHub:

# Install
if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/ggcorrplot")

41.2.2 Compute a correlation matrix

library("ggcorrplot")
# Compute a correlation matrix
mydata <- mtcars[, c(1,3,4,5,6,7)]
corr <- round(cor(mydata), 1)
head(corr[, 1:6], 3)

## mpg disp hp drat wt qsec

## mpg 1.0 -0.8 -0.8 0.7 -0.9 0.4
## disp -0.8 1.0 0.8 -0.7 0.9 -0.4
## hp -0.8 0.8 1.0 -0.4 0.7 -0.7

# Compute a matrix of correlation p-values

p.mat <- cor_pmat(mydata)
head(p.mat[, 1:4], 3)

## mpg disp hp drat

## mpg 0.000000e+00 9.380327e-10 1.787835e-07 1.776240e-05
## disp 9.380327e-10 0.000000e+00 7.142679e-08 5.282022e-06
## hp 1.787835e-07 7.142679e-08 0.000000e+00 9.988772e-03
230 CHAPTER 41. CORRELATION MATRIX VISUALIZATION

41.2.3 Correlation matrix visualization

# Visualize the correlation matrix

# --------------------------------
# method = "square" (default)
ggcorrplot(corr)

# Reordering the correlation matrix

# --------------------------------
# using hierarchical clustering
ggcorrplot(corr, hc.order = TRUE, outline.col = "white")

Corr Corr
qsec 1.0 drat 1.0
wt mpg
0.5 0.5
drat qsec
hp 0.0 wt 0.0
disp -0.5 disp -0.5
mpg hp
-1.0 -1.0
di g
sp

dr p
at
qs t
ec

di p
sp
qs wt
m c
dr g
at
w

e
p

p
m

# Types of correlogram layout and customization

# --------------------------------
# Add correlation coefficients
ggcorrplot(corr, hc.order = TRUE,
type = "lower", # get the lower triangle
outline.col = "white",
ggtheme = ggplot2::theme_bw, # change theme
colors = c("#6D9EC1", "white", "#E46726"), # change color palette
lab = TRUE # Add correlation coefficients
)

# Add correlation significance level

# --------------------------------
41.2. GGCORRPLOT 231

# Argument p.mat
# Barring the no significant coefficient
ggcorrplot(corr, hc.order = TRUE,
type = "lower", p.mat = p.mat)

Corr Corr
mpg 0.7 mpg 1.0
1.0
qsec 0.4 0.1 qsec 0.5
0.5
wt -0.2-0.9-0.7 wt 0.0
0.0
disp
disp 0.9 -0.4-0.8-0.7
-0.5
-0.5
hp
hp 0.8 0.7 -0.7-0.8-0.4 -1.0
-1.0
sp

qs t
ec
pg
at

sp

qs t
ec
pg
at
w

w
dr

dr
di

di
m

m
Chapter 42

Plotting Survival Curves

Survival analysis focuses on the expected duration of time until occurrence of an

event of interest. However, this failure time may not be observed within the study
time period, producing the so-called censored observations.
The R package survival fits and plots survival curves using R base graphs.

Here, we developed and present the survminer R package for drawing survival
curves using ggplot2 system.

42.1 Fitting survival curves

1. The R package survival is required. It can be installed as follow:

install.packages("survival")

2. Data set: lung data set from survival package:

data(lung, package = "survival")

# head(lung)

The data above includes:

232
42.2. DRAWING SURVIVAL CURVES WITH SURVMINER 233

time: Survival time in days

status: censoring status 1 = censored, 2 = dead
sex: Male = 1; Female = 2

3. Fitting survival curves

library("survival")
fit <- survfit(Surv(time, status) ~ sex, data = lung)

42.2 Drawing survival curves with survminer

The R package survminer contains the function ggsurvplot() for easily drawing
beautiful and ready-to-publish survival curves using ggplot2. ggsurvplot() includes
also some options for displaying the p-value and the number at risk table, under
the survival curves. survminer can be installed either from CRAN or GitHub.

Install from CRAN:

install.packages(survminer)

Install the latest version of survminer from GitHub:

if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/survminer")

Loading

library("survminer")
234 CHAPTER 42. PLOTTING SURVIVAL CURVES

42.2.1 ggsurvplot: Drawing survival curves

42.2.1.1 Basic plots

# Drawing survival curves

ggsurvplot(fit)

Strata + sex=1 + sex=2

1.00
++
++
Survival probability

0.75 +++++
+ ++++
+++ ++
++
0.50 ++ ++++
++
+ +++
+++
+++
0.25 +
+
+++ +
++
0.00
0 250 500 750 1000
Time

42.2.1.2 Customize survival curves

ggsurvplot(fit, size = 1, # change line size

palette = c("#E7B800", "#2E9FDF"), # custom color palette
conf.int = TRUE, # Add confidence interval
pval = TRUE, # Add p-value
risk.table = TRUE, # Add risk table
risk.table.col = "strata", # Risk table color by groups
ggtheme = theme_bw() # Change ggplot2 theme
)
42.2. DRAWING SURVIVAL CURVES WITH SURVMINER 235

Strata + sex=1 + sex=2

1.00
++
++
Survival probability

0.75 +++++
+ ++++
+++ ++
++ +
0.50 ++ +++
+++
+ +
+++++
+++
0.25 +
p = 0.0013
+
+++ +
++
0.00
0 250 500 750 1000
Time
Number at risk by time
Strata

sex=1 138 62 20 7 2
sex=2 90 53 21 3 0
0 250 500 750 1000
Time
Note that, allowed values, for the argument palette, include "hue" for the default
hue color scale; "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues",
"Dark2", ...; or custom color palette e.g. c("blue", "red").

Other useful arguments are also available in ggsurvplot (see ?ggsurvplot).

Chapter 43

References and further reading

43.1 Extensions to ggplot2: R packages and func-

tions
factoextra: factoextra : Extract and Visualize the outputs of a multi-
variate analysis. factoextra provides some easy-to-use functions to extract
and visualize the output of PCA (Principal Component Analysis), CA (Corre-
spondence Analysis) and MCA (Multiple Correspondence Analysis) functions
from several packages (FactoMineR, stats, ade4 and MASS). It contains also
many functions for simplifying clustering analysis workflows. Ggplot2 plotting
system is used.

ggfortify: Define fortify and autoplot functions to allow ggplot2 to handle

some popular R packages. These include plotting 1) Matrix; 2) Linear Model
and Generalized Linear Model; 3) Time Series; 4) PCA/Clustering; 5) Survival
Curve; 6) Probability distribution

GGally: GGally extends ggplot2 by providing several functions including pair-

wise correlation matrix, scatterplot plot matrix, parallel coordinates
plot, survival plot and several functions to plot networks.

ggRandomForests: Graphical analysis of random forests with the random-

ForestSRC and ggplot2 packages.

ggdendro: Create dendrograms and tree diagrams using ggplot2

ggmcmc: Tools for Analyzing MCMC Simulations from Bayesian Inference

236
43.2. CHEAT SHEETS 237

ggthemes: Package with additional ggplot2 themes and scales

43.2 Cheat Sheets

Be Awesome in ggplot2: A Practical Guide to be Highly Effective
Data Visualization with ggplot2, RStudio cheat sheet
Beautiful plotting in R: A ggplot2 cheatsheet

43.3 References
This book was written in R Markdown inside RStudio. knitr and pandoc converted
the raw Rmarkdown to pdf. This version of the book was built with R (ver. x86_64-
apple-darwin13.4.0, x86_64, darwin13.4.0, x86_64, darwin13.4.0, , 3, 2.3, 2015, 12,
10, 69752, R, R version 3.2.3 (2015-12-10), Wooden Christmas-Tree), ggplot2 (ver.
2.1.0) and dplyr (ver. 0.4.3)

Hadley Wickman. Elegant graphics for data analysis. Springer 2009. http:
//ggplot2.org/book/
Hadley Wickman. ggplot2 official documentation. http://docs.ggplot2.org/
current/
Winston Chang. R graphics cookbook. OReilly 2012. http://www.cookbook-r.
com/
Alboukadel Kassambara. Data analysis and visualization. http://www.sthda.
com/english/wiki/ggplot2-introduction