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table of contents

Preface ix
1. R Basics 1
1.1. Installing a Package 1
1.2. Loading a Package 2
1.3. Loading a Delimited Text Data File 3
1.4. Loading Data from an Excel File 4
1.5. Loading Data from an SPSS File 5
2. Quickly Exploring Data 7
2.1. Creating a Scatter Plot 7
2.2. Creating a Line Graph 9
2.3. Creating a Bar Graph 11
2.4. Creating a Histogram 13
2.5. Creating a Box Plot 15
2.6. Plotting a Function Curve 17
3. Bar Graphs 19
3.1. Making a Basic Bar Graph 19
3.2. Grouping Bars Together 22
3.3. Making a Bar Graph of Counts 25
3.4. Using Colors in a Bar Graph 27
3.5. Coloring Negative and Positive Bars Differently 29
3.6. Adjusting Bar Width and Spacing 30
3.7. Making a Stacked Bar Graph 32
3.8. Making a Proportional Stacked Bar Graph 35
3.9. Adding Labels to a Bar Graph 38
3.10. Making a Cleveland Dot Plot 42
4. Line Graphs 49
4.1. Making a Basic Line Graph 49
4.2. Adding Points to a Line Graph 52
4.3. Making a Line Graph with Multiple Lines 53
4.4. Changing the Appearance of Lines 58
4.5. Changing the Appearance of Points 59
4.6. Making a Graph with a Shaded Area 62
4.7. Making a Stacked Area Graph 64
4.8. Making a Proportional Stacked Area Graph 67
4.9. Adding a Confidence Region 69
5. Scatter Plots 73
5.1. Making a Basic Scatter Plot 73
5.2. Grouping Data Points by a Variable Using Shape or Color 75
5.3. Using Different Point Shapes 77
5.4. Mapping a Continuous Variable to Color or Size 80
5.5. Dealing with Overplotting 84
5.6. Adding Fitted Regression Model Lines 89
5.7. Adding Fitted Lines from an Existing Model 94
5.8. Adding Fitted Lines from Multiple Existing Models 97
5.9. Adding Annotations with Model Coefficients 100
5.10. Adding Marginal Rugs to a Scatter Plot 103
5.11. Labeling Points in a Scatter Plot 104
5.12. Creating a Balloon Plot 110
5.13. Making a Scatter Plot Matrix 112
6. Summarized Data Distributions 117
6.1. Making a Basic Histogram 117
6.2. Making Multiple Histograms from Grouped Data 120
6.3. Making a Density Curve 123
6.4. Making Multiple Density Curves from Grouped Data 126
6.5. Making a Frequency Polygon 129
6.6. Making a Basic Box Plot 130
6.7. Adding Notches to a Box Plot 133
6.8. Adding Means to a Box Plot 134
6.9. Making a Violin Plot 135
6.10. Making a Dot Plot 139
6.11. Making Multiple Dot Plots for Grouped Data 141
6.12. Making a Density Plot of Two-Dimensional Data 143
7. Annotations 147
7.1. Adding Text Annotations 147
7.2. Using Mathematical Expressions in Annotations 150
7.3. Adding Lines 152
7.4. Adding Line Segments and Arrows 155
7.5. Adding a Shaded Rectangle 156
7.6. Highlighting an Item 157
7.7. Adding Error Bars 159
7.8. Adding Annotations to Individual Facets 162
8. Axes 167
8.1. Swapping X- and Y-Axes 167
8.2. Setting the Range of a Continuous Axis 168
8.3. Reversing a Continuous Axis 170
8.4. Changing the Order of Items on a Categorical Axis 172
8.5. Setting the Scaling Ratio of the X- and Y-Axes 174
8.6. Setting the Positions of Tick Marks 177
8.7. Removing Tick Marks and Labels 178
8.8. Changing the Text of Tick Labels 180
8.9. Changing the Appearance of Tick Labels 182
8.10. Changing the Text of Axis Labels 184
8.11. Removing Axis Labels 185
8.12. Changing the Appearance of Axis Labels 187
8.13. Showing Lines Along the Axes 189
8.14. Using a Logarithmic Axis 190
8.15. Adding Ticks for a Logarithmic Axis 196
8.16. Making a Circular Graph 198
8.17. Using Dates on an Axis 204
8.18. Using Relative Times on an Axis 207
9. Controlling the Overall Appearance of Graphs 211
9.1. Setting the Title of a Graph 211
9.2. Changing the Appearance of Text 213
9.3. Using Themes 216
9.4. Changing the Appearance of Theme Elements 218
9.5. Creating Your Own Themes 221
9.6. Hiding Grid Lines 222
10. Legends 225
10.1. Removing the Legend 225
10.2. Changing the Position of a Legend 227
10.3. Changing the Order of Items in a Legend 229
10.4. Reversing the Order of Items in a Legend 231
10.5. Changing a Legend Title 232
10.6. Changing the Appearance of a Legend Title 235
10.7. Removing a Legend Title 236
10.8. Changing the Labels in a Legend 237
10.9. Changing the Appearance of Legend Labels 239
10.10. Using Labels with Multiple Lines of Text 240
11. Facets 243
11.1. Splitting Data into Subplots with Facets 243
11.2. Using Facets with Different Axes 246
11.3. Changing the Text of Facet Labels 246
11.4. Changing the Appearance of Facet Labels and Headers 250
12. Using Colors in Plots 251
12.1. Setting the Colors of Objects 251
12.2. Mapping Variables to Colors 252
12.3. Using a Different Palette for a Discrete Variable 254
12.4. Using a Manually Defined Palette for a Discrete Variable 259
12.5. Using a Colorblind-Friendly Palette 261
12.6. Using a Manually Defined Palette for a Continuous Variable 263
12.7. Coloring a Shaded Region Based on Value 264
13. Miscellaneous Graphs 267
13.1. Making a Correlation Matrix 267
13.2. Plotting a Function 271
13.3. Shading a Subregion Under a Function Curve 272
13.4. Creating a Network Graph 274
13.5. Using Text Labels in a Network Graph 278
13.6. Creating a Heat Map 281
13.7. Creating a Three-Dimensional Scatter Plot 283
13.8. Adding a Prediction Surface to a Three-Dimensional Plot 285
13.9. Saving a Three-Dimensional Plot 289
13.10. Animating a Three-Dimensional Plot 291
13.11. Creating a Dendrogram 291
13.12. Creating a Vector Field 294
13.13. Creating a QQ Plot 299
13.14. Creating a Graph of an Empirical Cumulative Distribution Function 301
13.15. Creating a Mosaic Plot 302
13.16. Creating a Pie Chart 307
13.17. Creating a Map 309
13.18. Creating a Choropleth Map 313
13.19. Making a Map with a Clean Background 317
13.20. Creating a Map from a Shapefile 319
14. Output for Presentation 323
14.1. Outputting to PDF Vector Files 323
14.2. Outputting to SVG Vector Files 325
14.3. Outputting to WMF Vector Files 325
14.4. Editing a Vector Output File 326
14.5. Outputting to Bitmap (PNG/TIFF) Files 327
14.6. Using Fonts in PDF Files 330
14.7. Using Fonts in Windows Bitmap or Screen Output 332
15. Getting Your Data into Shape 335
15.1. Creating a Data Frame 336
15.2. Getting Information About a Data Structure 337
15.3. Adding a Column to a Data Frame 338
15.4. Deleting a Column from a Data Frame 338
15.5. Renaming Columns in a Data Frame 339
15.6. Reordering Columns in a Data Frame 340
15.7. Getting a Subset of a Data Frame 341
15.8. Changing the Order of Factor Levels 343
15.9. Changing the Order of Factor Levels Based on Data Values 344
15.10. Changing the Names of Factor Levels 345
15.11. Removing Unused Levels from a Factor 347
15.12. Changing the Names of Items in a Character Vector 348
15.13. Recoding a Categorical Variable to Another Categorical Variable 349
15.14. Recoding a Continuous Variable to a Categorical Variable 351
15.15. Transforming Variables 352
15.16. Transforming Variables by Group 354
15.17. Summarizing Data by Groups 357
15.18. Summarizing Data with Standard Errors and Confidence Intervals 361
15.19. Converting Data from Wide to Long 365
15.20. Converting Data from Long to Wide 368
15.21. Converting a Time Series Object to Times and Values 369
A. Introduction to ggplot2 373
Index 385