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Index.First(), 131
abbreviate(), 137
annotation, 1, 26, 151
axis, see axis annotation
mathematical, see mathematical annotation
Arguments..., 31–33, 216, 232, 233, 241, 253
abbreviate, 137
alpha, 52
as.table, 20, 119, 131
aspect, 19, 24, 41, 68, 92, 105, 131,
141, 143, 184, 245
auto.key, 5, 26, 27, 61, 126, 152, 158,
159, 176, 199
axis, 144
axis.components, 130
between, 24, 85, 130, 131border, 32, 33
box.ratio, 183bw, 36
cex, 129
clip, 129
coef, 47
col, 80
col.regions, 240, 241
color, 121colorkey, 152, 155, 156
column, 217
common.scale, 88
data, 3, 5, 14, 41, 73, 86, 165, 166,
170, 173, 232, 247, 250
default.scales, 138, 139

device, 121
distance, 93
distribute.type, 80, 81
do.out, 47
drape, 155draw, 75
draw.key, 26
drop.unused.levels, 176echo, 7f.value, 41
fill, 243
fontsize, 129
fun, 199
grid.pars, 129
groups, 5, 24, 57, 73, 75, 77, 79, 80,
86, 96, 156, 159, 165, 166, 168,
176, 199, 253
highlight, 221horizontal, 52, 75, 77, 182
index.cond, 63, 193, 206
jitter.data, 52, 199
kern, 36
key, 26, 75, 129, 130, 152–154, 156,
157, 160
labels, 220
layout, 20, 21, 24, 206
layout.heights, 129, 130
layout.widths, 129, 130
legend, 161, 162
levels, 187
lines, 157
lty, 80main, 26, 129, 151

260

Index

more, 203, 204
name, 125
new, 121
newpage, 203, 204
outer, 102, 168
overlap, 178
packet.panel, 203
page, 26, 131, 162, 218
panel, 30, 31, 110, 130
panel.3d.cloud, 110, 241
panel.3d.wireframe, 110, 241
panel.aspect, 92
panel.groups, 231
panel.height, 203
panel.width, 203
panel.xyplot, 75
par.settings, 125, 126, 203
par.strip.text, 197
pch, 94
perspective, 93
plot.args, 203
plot.points, 4, 36
points, 157
position, 203, 204prefix, 217
prepanel, 63, 134, 141
pscales, 85, 86, 139
R.mat, 93
rectangles, 157
ref, 4
relation, 129, 130, 190
retain, 122row, 217
scales, 29, 63, 94, 111, 134–136,
138–142, 144, 146, 150, 155
screen, 93
shrink, 109
skip, 24space, 159
split, 203, 204
stack, 59
strip, 28, 130, 131, 193, 196
strip.left, 28, 193, 197
style, 196
sub, 26, 130, 151
subscripts, 71, 73, 159, 168, 216,
219, 220, 232
subset, 5, 44, 159, 165, 166, 173, 176,
232, 253superpanel, 86
text, 157
theme, 121, 122, 125, 131
Titanic, 29
type, 39, 57, 63, 75, 77–81, 85, 96,146, 199, 230
value, 125
varnames, 86
varwidth, 47
x, 3, 232, 247, 250
xlab, 26, 130, 140, 151
xlim, 29, 92, 141
xscale.components, 144, 146, 147y, 232ylab, 26, 140, 151
ylim, 29, 92, 141
yscale.components, 144, 146zlab, 140, 151zlim, 92, 94
zoom, 94
argument passing, 33, 73, 199, 232, 252
arranging plots, 7, 179, 203
arrows(), 230
as.data.frame.table(), 55, 100
asinh(), 83
aspect ratio, 19, 28, 42, 57, 68, 92, 99,
143, 144, 184, 245, 249
attach(), 14
averaged shifted histogram, 39axis(), 211, 215
axis.default(), 135, 149
axis annotation, 2, 28, 81, 94, 133, 135,173
logarithmic, 144
three-dimensional, 139
axis breaks, 183
axis function, 135
axTicks(), 147
banking, 19, 42, 143–145, 184, 249
banking(), 143bar charts, 29, 31, 57, 167
three-dimensional, 109
barchart(), 9, 30, 31, 33, 52, 55, 59,
63, 65, 182, 202, 248, 253
bounding box (3-D), 92
box(), 211
box-and-whisker plots, 47, 179, 182, 237
boxcox(), 42

Indexboxplot(), 215
bwplot(), 9, 46, 47, 52, 182, 183categorical data, xi, 65
choropleth maps, see maps
Classes
POSIXct , 137
dendrogram , 161
expression , 26
factor , 63
flowSet , 250
formula , 3, 13, 14, 248, 250
matrix , 56, 107
shingle , 202
stl , 248, 250
table , 55, 59
trellis , 6, 7, 15, 16, 18–20, 31, 33, 95,
133, 140, 158, 179, 201–204, 206,
208, 209, 211, 215–217, 221, 232
ts , 187
classes, see object-oriented features
clipping, 129, 141, 231
cloud(), 9, 28, 91, 92, 96, 102, 109, 110,
126, 133, 139, 151, 241, 244
coercion, 52, 182
color, ix, 113, 120
conditioning variable, 3, 14
continuous random variables, 35
contour plots, 98, 241
contourplot(), 9, 91, 99, 105, 107
coplot(), 210
correlation matrices, 105, 238
corrgrams, 238
CRAN, x
cumulative distribution function, 35
current.column(), 96, 231
current.panel.limits(), 231
current.row(), 96, 231
curve(), 230
customizations, see settings
persistent, 131
cut(), 15, 67, 69, 71
cut-and-stack plots, 143, 184, 248
cutAndStack(), 248
datalarge, see large data
managing, 14, 98, 165, 249
data(), 2

261

Datasets
ancestry, 243barley, 52, 53
beavers, 172
biocAccess, 143, 211, 248
Car93, 157
Cars93, 108, 161
Chem97, 5, 35, 37, 40, 47, 53, 63, 100,
108, 110, 165
Earthquake, 78, 144environmental, 100
faithful, 36
Gcsemv, 169
GvHD, 250, 251
gvhd10, 37, 49, 83, 88, 90
mtcars, 86–89
Oats, 17, 19, 20, 27
postdoc, 59, 61
quakes, 50, 51, 67, 71, 91, 177
SeatacWeather, 79
state.region, 85, 161
state.x77, 207
Titanic, 166, 173
USAge.df, 114, 174
USArrests, 84, 85, 161
USCancerRates, 193, 246
VADeaths, 55, 56, 122, 254
volcano, 99, 100, 105, 107data rectangle, 28, 92, 134
dcopula(), 110
dendrogramGrob(), 161, 162
dendrograms, 108, 161
density(), 36, 37, 235
densityplot(), 4, 7, 9, 35, 36, 232, 235,
250, 251
density function, 35
density plots, 4, 24, 35, 235, 249
dev.print(), 120
devices, see graphics devices
dimnames(), 202, 211
discrete distributions, 53
discrete random variables, 63
distribution function, see cumulative
distribution function
dnorm(), 35
do.call(), 221
dotplot(), 9, 13, 52, 55–57, 77, 193,
248
dot plots, 55, 122, 184, 187, 203, 223

262

Index

downViewport(), 217
draw.colorkey(), 75, 152, 154–156
draw.key(), 26, 152, 156, 161, 218
dropping unused levels, 159, 176
dynamic manipulation, 95
ecdfplot(), 44
empirical CDF, 44
equal.count(), 16, 71, 178, 184eval.parent(), 252
expand.grid(), 102
expression(), 26, 200
expressions, see mathematical annotation
factor(), 187
factors, 15
false color level plots, see level plotsfor(), 7
formula interface, 3, 13, 54, 166, 170
fractions(), 146
generic functions, see object-oriented
featuresgetOption(), 131
GGobi, xi
glm(), 165, 173
graphical parameters, 1, 119, 123
specifying, 123graphical primitives, 229
graphics devices, 120
Grid graphical objects, see grob
Grid graphics, see Packages, grid
grid.circle(), 239
grid.edit(), 215
grid.locator(), 216, 217, 219
grid.points(), 230
grid.polygon(), 239
grid.text(), 230
grob, 26, 151, 152, 154, 155, 161, 162,
215
grouping, see superposition
hclust(), 108, 161
heatmap(), 163
heatmaps, 161
hexagonal binning, 83, 251
hexbinplot(), 83, 251, 252
high-level functions, 1, 9

histogram(), 3, 4, 7, 9, 30, 39, 248
histograms, 2, 39
hypocycloid, 232, 233
hypotrochoid, 232
identify(), 216
indexing, 71, 173, 206interaction, 86, 211, 216
jittering, 36, 52, 142, 177, 199
kernel density estimate, 36
key, see legends
labels, 26, 151
large data, 37, 49, 82, 88, 249
lattice.getOption(), 131
lattice.options(), 131, 141
layout, 15, 16, 20, 47, see arranging
plots
legends, 26, 75, 148, 152level plots, 98, 113, 161, 238
level.colors(), 73, 239, 241
levelplot(), 9, 91, 99, 105, 107, 108,
111, 155, 156, 163, 240, 241, 248
levels(), 140
library(), 2, 131
lines(), 215, 230lm(), 165, 173
locator(), 216log(), 83
log-spline density estimate, 235
logarithm, see transformations
long format, 166
ltransform3dMatrix(), 93
ltransform3dto3d(), 241
make.groups(), 170–172
map(), 243, 246
mapplot(), 245, 246, 251
maps, 98, 242
match.call(), 252
mathematical annotation, 26, 137, 146,
151, 200
mean–difference plots, 208
methods, see object-oriented features
new, see new methods
multipanel conditioning, 2, 3, 14
native coordinate system, 134

Indexnew displays, 251
new methods, 247
nonstandard evaluation, 165, 252
object-oriented features, 6, 13, 33, 56,
179, 201, 247
OpenGL, xi
options(), 131
orthogonal projection, 93
Packagescoda, 248
colorspace, 120
copula, x, 110
ellipse, x, 238
flowCore, x
flowViz, x, 250
ggplot, xi
ggplot2, xi
grid, x, xi, 26, 127, 129, 151, 152, 162,
203, 206, 215–217, 219, 229–231,
239, 252
gridBase, x, 252, 254
hexbin, x, 83, 251, 252
Hmisc, 247
lattice, 242, 248, 250
latticeExtra, x, 37, 44, 53, 59, 79, 109,
114, 143, 161, 174, 193, 210, 224,
242, 243, 246, 248, 251
locfit, x, 78, 80, 100
logspline, x, 235
mapproj, x, 246
maps, x, 242
MASS, x, 42, 99, 146
MEMSS, x, 77
mlmRev, x, 2, 169nlme, 247
playwith, xi, 215
RColorBrewer, x, 120, 243
rggobi, xi, 242
rgl, xi, 95, 242
vcd, xi, 65
zoo, 248
packages (installing), x
packet, 15, 28, 73, 95, 133
packet order, 18, 203packet.number(), 216, 221, 231
packet.panel.default(), 203
panel, 2263

panel function, 4, 30, 229, 252
three-dimensional, 96
panel order, 18, 203
panel.3dbars(), 109
panel.3dscatter(), 241
panel.3dwire(), 241
panel.abline(), 230
panel.arrows(), 230
panel.average(), 75, 199, 231
panel.axis(), 149
panel.barchart(), 31–33, 128
panel.bwplot(), 47, 49, 126, 183, 231
panel.cloud(), 110, 128
panel.curve(), 230
panel.densityplot(), 36, 128, 232
panel.dotplot(), 126
panel.fill(), 230
panel.grid(), 32, 75, 129, 230
panel.histogram(), 128
panel.identify(), 216, 219, 220
panel.identify.qqmath(), 219, 221
panel.levelplot(), 109, 128, 155
panel.lines(), 230
panel.link.splom(), 219, 221
panel.lmline(), 75, 136, 230
panel.locfit(), 80
panel.loess(), 75, 230
panel.mathdensity(), 230
panel.number(), 81, 208, 231
panel.pairs(), 86, 139
panel.parallel(), 88
panel.points(), 230
panel.polygon(), 230, 243, 245
panel.qqmathline(), 221, 230
panel.rect(), 230
panel.rug(), 169, 230
panel.segments(), 230
panel.splom(), 67, 84
panel.stripplot(), 52, 199
panel.superpose(), 75, 80, 231
panel.text(), 129, 230
panel.violin(), 49, 231
panel.wireframe(), 128, 155
panel.xyplot(), 67, 75, 77, 78, 80, 83,
84, 128, 199, 231
parallel(), 9, 54, 67, 88
parallel coordinates plots, 87
pdf(), 121, 122, 132
persp(), 93

264

Index

perspective projection, 93
pie(), 254
pie charts, 57, 252
piechart(), 253plot(), 7, 179, 202–204, 206, 215, 248
plot types, 75
plotting
automatic, 6suppression of, 7png(), 121
pnorm(), 35
points(), 230
polygon(), 230, 243
postscript(), 122, 132predict(), 102
prepanel.lmline(), 144
prepanel.loess(), 144, 146
prepanel.qqmathline(), 144
prepanel function, 28, 133, 134, 140, 142
pretty(), 149
primary variable, 4, 14, 168
print(), 6, 7, 202, 203, 215
probability mass function, 53
projection, 91, 241, 244
prop.table(), 59
qnorm(), 35
qq(), 9, 44, 47, 54, 208
qqmath(), 9, 40, 41, 54, 144, 208, 221,
230, 248
quantile function, 35
quantile plots, 40, 43, 170, 171, 181,
196, 218
two-sample, 44, 208
range(), 140rect(), 230
reorder(), 63, 187, 190
reordering, 61, 108, 187
require(), 131
reshape(), 168
reshaping, 166
residuals (visualizing), 52, 198, 248
resizePanels(), 193, 206, 224
rootogram(), 53
roulettes, 233
Rows(), 156, 157
rug(), 230

S-PLUS, vii, x, 153, 230
S3, 201, 248, 249
S4, 201, 247, 249, 250
scales, 2, 28, 133, 183, 193
combining, 28
scatter-plot matrices, 84, 100, 221
scatter plots, 16, 67, 82, 144, 157, 160,
169, 173, 177, 193, 219
three-dimensional, 91
seekViewport(), 217
segments(), 230settings
graphical, 27, 119, 158
non-graphical, 131
shingle(), 178, 184
shingles, 15, 71, 177
show.settings(), 128, 129
simpleKey(), 157, 158
simpleTheme(), 126
source(), 7
Spirograph, 232
splom(), 9, 28, 54, 67, 77, 84–86, 88,
133, 139, 221
spread–location plots, 52
square root transformation, 83, 108,
181, 251
stacked bar charts, 59
stereo viewing, 95
stl(), 248
str(), 123, 202
strip plots, 50
strip.custom(), 181, 197
strip.default(), 126, 196, 197
stripplot(), 9, 52, 77, 182, 199
strips, 2, 28, 181, 193, 210
subset(), 159
subsetting, see indexing
summary(), 202, 204
superpanel function, 85
superposition, 5, 24, 79, 156
surfaces, 98, 241
mathematical, 110
parameterized, 111
table(), 55, 248
tables, 55, 98
terrain.colors(), 115
text(), 230
textGrob(), 151

Indexthemes, 120
three-dimensionalplots, 91
projection, see projection
tick marks, 135, 138
major, 146
minor, 146
time-series plots, 143, 148, 174, 175,
184, 248
tmd(), 208
traditional graphics, 1, 6, 120, 211, 215,
230, 252transformations
Box–Cox, 42, 165
logarithm, 78, 144, 190
power, 42transparency, 52, 82, 90, 138“trellis”objects as arrays, 16, 20, 95,
203, 206, 211
Trellis formula, see formula interface
Trellis graphics, x, 1
documentation, xtrellis.currentLayout(), 224, 231
trellis.device(), 121, 122, 125, 131
trellis.focus(), 216, 217, 219–221
trellis.last.object(), 206, 221
trellis.panelArgs(), 221
trellis.par.get(), 122, 125, 157
trellis.par.set(), 121, 122, 125, 203265

trellis.unfocus(), 217, 221
trellis.vpname(), 216, 217
Tukey mean–difference plots, seemean–difference plots
units (grid), 206
univariate distributions, 35, 63
update(), 20, 31, 33, 206
useOuterStrips(), 210, 211variance stabilizing transformation, 181
viewport(), 219
viewports, 216
violin plots, 47, 49
which.packet(), 216, 232
while(), 7, 219
wide format, 166
wireframe(), 9, 91, 99, 105, 107, 109,
110, 113, 126, 139, 151, 155, 156,
241, 242, 248
wireframe plots, 98, 241with(), 14, 161
xscale.components.default(), 146
xtabs(), 2, 55, 63, 248
xyplot(), 9, 16, 27, 63, 67, 69, 73, 75,
77, 80, 157, 183, 201, 208, 219,
232, 247–250