Table of contents for Lattice : multivariate data visualization with R / Deepayan Sarkar.


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1   Introduction ........................................... 1
1.1 Multipanel conditioning ................................  2
1.1.1  A  histogram  for every group  ........................  2
1.1.2 The Trellis call ................................. 3
1.1.3  Kernel density plots  ...............................  4
1.2  Superposition  ................... ....................  5
1.3  The  "trellis" object  ................  ...................  6
1.3.1  The missing Trellis display  .........................  7
1.3.2  Arranging multiple Trellis plots  .....................  7
1.4 Looking ahead ....................................... 7
Part I Basics
2   A Technical Overview of lattice ..........................  13
2.1 Basic usage ............................................. 13
2.1.1 The Trellis formula ................ .............. 13
2.1.2 The data argument .............................. 14
2.1.3 Conditioning................................. 14
2.1.4 Shingles ...................................... 15
2.2 Dimension and physical layout ............................ 16
2.2.1 Aspect ratio .................................. 19
2.2.2 Layout ....................................... 20
2.2.3 Fine-tuning the layout: between and skip ............ 24
2.3 Grouped displays ...................................... 24
2.4  Annotation: Captions, labels, and legends  ..................  26
2.4.1 More on legends ................................. 26
2.5 Graphing the data .................................. 28
2.5.1 Scales and axes ................................... 28
2.5.2 The panel function ................................ 30
2.5.3 The panel function demystified ..................... 31
2.6 Return value ...................................... 33
3   Visualizing Univariate Distributions ....................... 35
3.1 Density Plot ......................................... 35
3.2 Large datasets .......................................... 37
3.3 Histograms ........................................ 39
3.4 Normal Q-Q plots ...................................... 40
3.4.1 Normality and the Box-Cox transformation. .......... 42
3.4.2 Other theoretical Q-Q plots ......................... 43
3.5 The empirical CDF ..................................... 44
3.6  Two-sample Q-Q  plots ...................................  44
3.7 Box-and-whisker plots ................................... 47
3.7.1 Violin plots ... ............................... 47
3.8 Strip plots ............................................. 50
3.9 Coercion rules ......................................  52
3.10  Discrete distributions  ................  .................  53
3.11  A  note on the formula interface  ...........................  54
4   Displaying Multiway Tables ............................... 55
4.1  Cleveland  dot plot .......................................  55
4.2 Bar chart ......................................... 57
4.2.1 Manipulating order ............................... 61
4.2.2  Bar charts and  discrete distributions .................  63
4.3 Visualizing categorical data .............................. 65
5   Scatter Plots and Extensions .............................. 67
5.1 The standard scatter plot ..............................  67
5.2  Advanced indexing using subscripts ......................  71
5.3  Variants using the type argument  .........................  75
5.3.1  Superposition  and type  ............................  79
5.4 Scatter-plot variants for large data ......................... 82
5.5  Scatter-plot matrix  ......................................  84
5.5.1  Interacting with scatter-plot matrices ................  86
5.6 Parallel coordinates plot ................................. 87
6   Trivariate Displays .................................... 91
6.1  Three-dimensional scatter plots  ...........................  91
6.1.1 Dynamic manipulation versus stereo viewing .......... 95
6.1.2 Variants and panel functions ....................... 96
6.2  Surfaces and two-way tables  ..............................  98
6.2.1  Data preparation ..................................  99
6.2.2  Visualizing surfaces ........... ...... ............. 102
6.2.3 Visualizing discrete array data ...................... 105
6.3 Theoretical surfaces ...................................... 110
6.3.1 Parameterized surfaces ............................. 111
6.4  Choosing a palette for false-color plots ..................... 113
Part II Finer Control
7   Graphical Parameters and Other Settings ................. 119
7.1  The parameter system  ................................... 119
7.1.1 Themes ..........................................120
7.1.2 Devices .............   . .......................120
7.1.3  Initializing  a  graphics device ........................ 121
7.1.4 Reading and modifying a theme ..................... 122
7.1.5  Usage and  alternative forms  ........................ 125
7.1.6  The par. settings argument  ....................... 125
7.2 Available graphical parameters ............................ 126
7.2.1  Nonstandard  settings  .............................. 129
7.3  Non-graphical options .................................... 131
7.3.1 Argument defaults ............................... 131
7.4  Making customizations persistent .......................... 131
8   Plot Coordinates and Axis Annotation .................... 133
8.1 Packets and the prepanel function ......................... 133
8.2 The scales argument ................................ 134
8.2.1  Relation ..........................................134
8.2.2  Axis annotation: Ticks and  labels  ................... 135
8.2.3  Defaults ................... .... ...................138
8.2.4 Three-dimensional displays: cloud() and wireframe() 139
8.3  Limits and aspect ratio  .................. ............... 140
8.3.1  The prepanel function revisited  ..................... 140
8.3.2  Explicit specification  of limits ....................... 141
8.3.3  Choosing aspect ratio by banking  ................... 1.43
8.4 Scale components and the axis function .................... 144
8.4.1 Components ...................................... 144
8.4.2 Axis ........................................148
9   Labels and Legends ........................................151
9.1 Labels ..............................................151
9.2  Legends  ................................................152
9.2.1  Legends as grid graphical objects .................... .152
9.2.2 The colorkey argument ........................... 155
9.2.3  The  key  argument ....... ............ ............ 156
9.2.4 The problem with settings, and the auto.key argument 158
9.2.5 Dropping unused levels from groups ................. 159
9.2.6 A more complicated example ....................... 159
9.2.7 Further control: The legend argument ............... 161
9.3 Page annotation .........................................162
10 Data Manipulation and Related Topics .................... 165
10.1 Nonstandard evaluation ................ ............... 165
10.2 The extended formula interface ........................... 166
10.3 Combining data sources with make. groups() ............... 170
10.4 Subsetting ..............................................173
10.4.1  Dropping  of factor levels  ........................... 176
10.5 Shingles and related utilities .............................. 177
10.5.1  Coercion  to factors and shingles ..................... 182
10.5.2  Using shingles for axis breaks ....................... 183
10.5.3 Cut-and-stack plots ............................... 184
10.6  Ordering levels of categorical variables  ......... ............. 187
10.7  Controlling the appearance of strips  ....................... 193
10.8  An Example Revisited  ................................... 198
11 Manipulating the "trellis" Object ....................... 201
11.1 Methods for "trellis" objects .............. ...........201
11.2 The plot(), print(), and summary() methods ............. 202
11.3 The update () method and trellis.last. object () ......... 206
11.4 Tukey mean-difference plot ...........................  208
11.5 Specialized manipulations ............................  210
11.6 Manipulating the display ..............................  211
12 Interacting with Trellis Displays ........................ 215
12.1 The traditional graphics model ......................... 215
12.1.1 Interaction ....................................216
12.2 Viewports, trellis.vpname(), and trellis.focus() ....... 216
12.3  Interactive additions ..................................... 217
12.4 Other uses ............................................223
Part III Extending Trellis Displays
13 Advanced Panel Functions ............    ................... 229
13.1  Preliminaries  ...........................................229
13.1.1  Building blocks for panel functions  .................. 229
13.1.2 Accessor functions ............................... 231
13.1.3  Arguments .......... ...... ...................... 232
13.2 A toy example: Hypotrochoids and hypocycloids ............ 232
13.3 Some more examples ................................... 235
13.3.1  An  alternative density  estimate  ..................... 235
13.3.2  A  modified box-and-whisker plot .................... 237
13.3.3 Corrgrams as customized level plots ................. 238
13.4 Three-dimensional projections ......................... 241
13.5 Maps ....................... .   ................... .....242
13.5.1  A  simple projection scheme ......................... 244
13.5.2 Maps with conditioning ......................... 245
14 New Trellis Displays ..................................     247
14.1 SS3 methods ..........    ........................... 248
14.2 S4 methods ............... .   ........................ 249
14.3 New functions .......................................251
14.3.1 A complete example: Multipanel pie charts ........... 252



Library of Congress subject headings for this publication: Lattice theory, R (Computer program language)Computer graphics