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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 visualizing

one continous/discrete variable: area plots, density plots, histogram plots,

frequency polygon, dot plots, ECDF and QQ plots.

Part III provides quick-start guides for plotting two continuous/discretes variables,

including :

• Scatter plots (chapter 12)

• Continuous bivariate distribution (chapter 13)

• Jitter plots of two discretes variables (chapter 14)

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.

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)

Alboukadel Kassambara is a Health – Biology Scientist with ten years work experiences in Cancer Biology and Bioinformatics.

He has extensive experiences in statistical and computational methods to identify prognostic and predictive biomarker signatures through integrative analysis of large-scale genomic and clinical data sets.

He created a bioinformatics web-tool named GenomicScape, for an easy gene expression data analysis and visualization.

He developed also a training website on data science, named STHDA, which contains many tutorials on data analysis and visualization using R software and packages.

He is the author of many popular R packages for multivariate data analysis, survival analysis and data visualization.

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
2 Introduction to ggplot2 29
2.1 What’s 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
11 Bar Plots of Counts 60
III Plot Two Variables - X & Y: Both Continuous or Discrete
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 Continuous
Y 84
14.1 Data format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
14.2 Plot types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
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
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
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
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
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
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