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Part II GRID GRAPHICS
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Part II GRID GRAPHICS
by Paul Murrell
R Graphics, 2nd Edition
Preliminaries
Series
Preface
What this book is about
Changes in the second edition
What this book is still not about
Who should read this book
Conventions used in this book
On the web
Version information
Acknowledgments
Chapter 1 An Introduction to R Graphics
1.1 R graphics examples
1.1.1 Standard plots
1.1.2 Trellis plots
1.1.3 The Grammar of Graphics
1.1.4 Specialized plots
1.1.5 General graphical scenes
1.2 The organization of R graphics
1.2.1 Types of graphics functions
1.2.2 Traditional graphics versus grid graphics
Figure 1.1
Figure 1.1
Figure 1.2
Figure 1.3
Figure 1.4
Figure 1.5
Figure 1.6
Figure 1.7
Figure 1.8
Figure 1.9
Figure 1.10
Figure 1.11
Figure 1.12
Figure 1.13
Figure 1.14
Part I TRADITIONAL GRAPHICS
Chapter 2 Simple Usage of Traditional Graphics
2.1 The traditional graphics model
2.2 The plot() function
2.3 Plots of a single variable
2.4 Plots of two variables
2.5 Plots of many variables
2.6 Arguments to graphics functions
2.6.1 Standard arguments to graphics functions
2.7 Specialized plots
2.8 Interactive graphics
Figure 2.1
Figure 2.1
Figure 2.2
Figure 2.3
Figure 2.4
Figure 2.5
Figure 2.6
Figure 2.7
Figure 2.8
Figure 2.9
Table 2.1
Table 2.1
Table 2.2
Table 2.3
Chapter 3 Customizing Traditional Graphics
3.1 The traditional graphics model in more detail
3.1.1 Plotting regions
Coordinate systems
3.1.2 The traditional graphics state
3.2 Controlling the appearance of plots
3.2.1 Colors
Fill patterns
3.2.2 Lines
3.2.3 Text
Text size
Specifying fonts
Justification of text
Rotating text
Multi-line text
3.2.4 Data symbols
3.2.5 Axes
3.2.6 Plotting regions
Outer margins
Figure regions
Figure margins
Plot regions
3.2.7 Clipping
3.2.8 Moving to a new plot
3.3 Arranging multiple plots
3.3.1 Using the traditional graphics state
3.3.2 Layouts
3.3.3 The split-screen approach
3.4 Annotating plots
3.4.1 Annotating the plot region
Graphical primitives
Graphical utilities
Missing values and non-finite values
3.4.2 Annotating the margins
3.4.3 Legends
3.4.4 Axes
3.4.5 Coordinate systems
The par() function
Overlaying output
3.4.6 Special cases
Obscure scales on axes
Functions that draw several plots
3D plots
3.5 Creating new plots
3.5.1 A simple plot from scratch
3.5.2 A more complex plot from scratch
3.5.3 Writing traditional graphics functions
Helper functions
Argument lists
Plot methods
A graphics function template
Figure 3.1
Figure 3.1
Figure 3.2
Figure 3.3
Figure 3.4
Figure 3.5
Figure 3.6
Figure 3.7
Figure 3.8
Figure 3.9
Figure 3.10
Figure 3.11
Figure 3.12
Figure 3.13
Figure 3.14
Figure 3.15
Figure 3.16
Figure 3.17
Figure 3.18
Figure 3.19
Figure 3.20
Figure 3.21
Figure 3.22
Figure 3.23
Figure 3.24
Figure 3.25
Figure 3.26
Figure 3.27
Figure 3.28
Table 3.1
Table 3.1
Table 3.2
Table 3.3
Table 3.4
Table 3.5
Part II GRID GRAPHICS
Chapter 4 Trellis Graphics: The lattice Package
4.1 The lattice graphics model
4.1.1 Why another graphics system?
4.2 lattice plot types
4.3 The formula argument and multipanel conditioning
4.4 The group argument and legends
4.5 The layout argument and arranging plots
4.6 The scales argument and labeling axes
4.7 The panel argument and annotating plots
4.7.1 Adding output to a lattice plot
4.8 par.settings and graphical parameters
4.9 Extending lattice plots
4.9.1 The latticeExtra package
Figure 4.1
Figure 4.1
Figure 4.2
Figure 4.3
Figure 4.4
Figure 4.5
Figure 4.6
Figure 4.7
Figure 4.8
Figure 4.9
Figure 4.10
Figure 4.11
Figure 4.12
Figure 4.13
Table 4.1
Table 4.1
Table 4.2
Table 4.3
Table 4.4
Chapter 5 The Grammar of Graphics: The ggplot2 Package
5.1 Quick plots
5.2 The ggplot2 graphics model
5.2.1 Why another graphics system?
5.2.2 An example data set
5.3 Data
5.4 Geoms and aesthetics
5.5 Scales
5.6 Statistical transformations
5.7 The group aesthetic
5.8 Position adjustments
5.9 Coordinate transformations
5.10 Facets
5.11 Themes
5.12 Annotating
5.13 Extending ggplot2
Figure 5.1
Figure 5.1
Figure 5.2
Figure 5.3
Figure 5.4
Figure 5.5
Figure 5.6
Figure 5.7
Figure 5.8
Figure 5.9
Figure 5.10
Figure 5.11
Figure 5.12
Figure 5.13
Figure 5.14
Figure 5.15
Table 5.1
Table 5.1
Table 5.2
Table 5.3
Table 5.4
Chapter 6 The grid Graphics Model
6.1 A brief overview of grid graphics
6.1.1 A simple example
6.2 Graphical primitives
6.2.1 Standard arguments
6.2.2 Clipping
6.3 Coordinate systems
6.3.1 Conversion functions
6.3.2 Complex units
6.4 Controlling the appearance of output
6.4.1 Specifying graphical parameter settings
6.4.2 Vectorized graphical parameter settings
6.5 Viewports
6.5.1 Pushing, popping, and navigating between viewports
Drawing between viewports
6.5.2 Clipping to viewports
6.5.3 Viewport lists, stacks, and trees
Viewport paths
6.5.4 Viewports as arguments to graphical primitives
6.5.5 Graphical parameter settings in viewports
6.5.6 Layouts
A simple layout
A layout with units
A nested layout
6.6 Missing values and non-finite values
6.7 Interactive graphics
6.8 Customizing lattice plots
6.8.1 Adding grid output to lattice output
6.8.2 Adding lattice output to grid output
6.9 Customizing ggplot2 output
6.9.1 Adding grid output to ggplot2 output
6.9.2 Adding ggplot2 output to grid output
Figure 6.1
Figure 6.1
Figure 6.2
Figure 6.3
Figure 6.4
Figure 6.5
Figure 6.6
Figure 6.7
Figure 6.8
Figure 6.9
Figure 6.10
Figure 6.11
Figure 6.12
Figure 6.13
Figure 6.14
Figure 6.15
Figure 6.16
Figure 6.17
Figure 6.18
Figure 6.19
Figure 6.20
Figure 6.21
Figure 6.22
Figure 6.23
Figure 6.24
Figure 6.25
Figure 6.26
Table 6.1
Table 6.1
Table 6.2
Table 6.3
Table 6.4
Chapter 7 The grid Graphics Object Model
7.1 Working with graphical output
7.1.1 Standard functions and arguments
7.2 Grob lists, trees, and paths
7.2.1 Graphical parameter settings in gTrees
7.2.2 Viewports as components of gTrees
7.2.3 Searching for grobs
7.3 Working with graphical objects off-screen
7.3.1 Capturing output
7.4 Placing and packing grobs in frames
7.4.1 Placing and packing off-screen
7.5 Other details about grobs
7.5.1 Calculating the sizes of grobs
7.5.2 Calculating the positions of grobs
7.5.3 Editing graphical context
7.6 Saving and loading grid graphics
7.7 Working with lattice grobs
7.8 Working with ggplot2 grobs
Figure 7.1
Figure 7.1
Figure 7.2
Figure 7.3
Figure 7.4
Figure 7.5
Figure 7.6
Figure 7.7
Figure 7.8
Figure 7.9
Figure 7.10
Figure 7.11
Figure 7.12
Figure 7.13
Table 7.1
Table 7.1
Chapter 8 Developing New Graphics Functions and Objects
8.1 An example
8.1.1 Modularity
8.2 Simple graphics functions
8.2.1 Embedding graphical output
8.2.2 Facilitating annotation
8.2.3 Editing output
8.2.4 Absolute versus relative sizes
8.3 Graphical objects
8.3.1 Overview of creating a new graphical class
8.3.2 Defining a new graphical class
Summary of creating a new graphical class
8.3.3 Validating grobs
Default validating behavior
The imageGrob example
8.3.4 Drawing grobs
Default drawing behavior
The imageGrob example
An ozGrob example
An ozImage example
8.3.5 Editing grobs
Default editing behavior
The imageGrob example
The ozGrob example
The ozImage example
The imageGrob example again
The ozImage example again
8.3.6 Querying grobs
Default sizing behavior
A ribbonLegend example
8.3.7 Pre-drawing and post-drawing
Default pre/post-drawing behavior
8.3.8 Summary of graphical object methods
8.3.9 Completing the example
8.3.10 Reusing graphical elements
8.3.11 Other details
Extending other grobs
Display lists
Calculations during drawing
Avoiding argument explosion
Mixing graphical functions and graphical objects
8.4 Debugging grid
Figure 8.1
Figure 8.1
Figure 8.2
Figure 8.3
Figure 8.4
Figure 8.5
Figure 8.6
Figure 8.7
Figure 8.8
Figure 8.9
Figure 8.10
Figure 8.11
Figure 8.12
Figure 8.13
Figure 8.14
Figure 8.15
Figure 8.16
Figure 8.17
Figure 8.18
Figure 8.19
Figure 8.20
Figure 8.21
Figure 8.22
Figure 8.23
Figure 8.24
Figure 8.25
Figure 8.26
Figure 8.27
Part III THE GRAPHICS ENGINE
Chapter 9 Graphics Formats
9.1 Graphics devices
9.2 Graphical output formats
9.2.1 Vector formats
PDF
PostScript
SVG
Windows Metafile
9.2.2 Raster formats
9.3 Including R graphics in other documents
9.3.1 LATEX
9.3.2 “Productivity” software
9.3.3 Web pages
9.4 Device-specific features
9.5 Multiple pages of output
9.6 Display lists
9.7 Extension packages
Table 9.1
Table 9.1
Table 9.2
Chapter 10 Graphical Parameters
10.1 Colors
10.1.1 Semitransparent colors
10.1.2 Converting colors
10.1.3 Color sets
10.1.4 Device Dependency of Color Specifications
10.2 Line styles
10.2.1 Line widths
10.2.2 Line types
10.2.3 Line ends and joins
10.3 Data symbols
10.4 Fonts
10.4.1 Font family
10.4.2 Font face
10.4.3 Multi-line text
10.4.4 Locales
10.5 Mathematical formulae
Figure 10.1
Figure 10.1
Figure 10.2
Figure 10.3
Figure 10.4
Table 10.1
Table 10.1
Table 10.2
Table 10.3
Part IV GRAPHICS PACKAGES
Chapter 11 Graphics Extensions
11.1 Tricks with text
11.1.1 Drawing formatted text on a plot
11.1.2 Avoiding text overlaps
11.2 Peculiar primitives
11.2.1 Confidence bars
11.3 Calculations on colors
11.3.1 The colorspace package
11.3.2 The RColorBrewer package
11.3.3 The munsell package
11.3.4 The dichromat package
11.4 Custom coordinates
11.4.1 Converting between traditional coordinate systems
11.4.2 Subplots
11.5 Atypical axes
Figure 11.1
Figure 11.1
Figure 11.2
Figure 11.3
Figure 11.4
Figure 11.5
Figure 11.6
Figure 11.7
Figure 11.8
Figure 11.9
Figure 11.10
Figure 11.11
Figure 11.12
Figure 11.13
Chapter 12 Plot Extensions
12.1 Venn diagrams
12.2 Chernoff faces
12.3 Ternary plots
12.3.1 Soil texture diagrams
12.4 Polar plots
12.4.1 Wind roses
12.5 Hexagonal binning
Figure 12.1
Figure 12.1
Figure 12.2
Figure 12.3
Figure 12.4
Figure 12.5
Figure 12.6
Figure 12.7
Chapter 13 Graphics for Categorical Data
13.1 The vcd package
13.2 XMM-Newton
13.3 Plots of categorical data
13.4 Categorical data on the y-axis
13.5 Visualizing contingency tables
13.6 Categorical plot matrices
13.7 Multipanel categorical plots
13.8 Customizing categorical plots
13.9 The vcdExtra package
Figure 13.1
Figure 13.1
Figure 13.2
Figure 13.3
Figure 13.4
Figure 13.5
Figure 13.6
Figure 13.7
Figure 13.8
Chapter 14 Maps
14.1 Map data
14.1.1 The maps package
14.1.2 Shapefiles
14.2 Map annotation
14.3 Complex polygons
14.4 Map projections
14.5 Raster maps
14.6 Other packages
Figure 14.1
Figure 14.1
Figure 14.2
Figure 14.3
Figure 14.4
Figure 14.5
Figure 14.6
Figure 14.7
Figure 14.8
Figure 14.9
Figure 14.10
Figure 14.11
Chapter 15 Node-and-edge Graphs
15.1 Creating graphs
15.1.1 The graph package
15.2 Graph layout and rendering
15.2.1 The Rgraphviz package
15.2.2 Graph attributes
15.2.3 Customization
15.2.4 Output formats
15.2.5 Hypergraphs
15.3 Other packages
15.3.1 The igraph package
15.3.2 The network package
15.4 Diagrams
15.4.1 The diagram and shape packages
Figure 15.1
Figure 15.1
Figure 15.2
Figure 15.3
Figure 15.4
Figure 15.5
Figure 15.6
Figure 15.7
Figure 15.8
Figure 15.9
Figure 15.10
Chapter 16 3D Graphics
16.1 3D graphics concepts
16.2 The Canterbury earthquake
16.3 Traditional graphics
16.4 lattice graphics
16.5 The scatterplot3d package
16.6 The rgl package
16.7 The vrmlgen package
Figure 16.1
Figure 16.1
Figure 16.2
Figure 16.3
Figure 16.4
Figure 16.5
Figure 16.6
Figure 16.7
Figure 16.8
Figure 16.9
Figure 16.10
Figure 16.11
Chapter 17 Dynamic and Interactive Graphics
17.1 Dynamic graphics
17.1.1 The animation package
17.2 Interactive graphics
17.2.1 Tools and techniques
17.2.2 The rggobi package
Tours
17.2.3 The iplots package
Developing new interactive plots
17.3 Graphics GUIs
17.3.1 GUIs for R
17.3.2 GUI toolkits
An interactive clock
The gWidgets package
17.4 Interactive graphics for the web
Figure 17.1
Figure 17.1
Figure 17.2
Figure 17.3
Figure 17.4
Figure 17.5
Figure 17.6
Figure 17.7
Figure 17.8
Figure 17.9
Figure 17.10
Figure 17.11
Figure 17.12
Figure 17.13
Figure 17.14
Figure 17.15
Figure 17.16
Chapter 18 Importing Graphics
18.1 The Moon and the tides
18.2 Importing raster graphics
18.2.1 Manipulating raster images
18.3 Importing vector graphics
18.3.1 The grImport package
18.3.2 Manipulating vector images
Figure 18.1
Figure 18.1
Figure 18.2
Figure 18.3
Figure 18.4
Figure 18.5
Figure 18.6
Table 18.1
Table 18.1
Chapter 19 Combining Graphics Systems
19.1 The gridBase package
19.1.1 Annotating traditional graphics using grid
19.1.2 Traditional graphics in grid viewports
19.1.3 Problems and limitations
Figure 19.1
Figure 19.1
Figure 19.2
Bibliography
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Chapter 3 Customizing Traditional Graphics
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Chapter 4 Trellis Graphics: The lattice Package
Part II
GRID GRAPHICS
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