Description Usage Arguments Value Note Author(s) See Also Examples
scatter2D and scatter3D
plot a (2- or 3 dimensional) dataset with a color variable as points or lines.
text3D
plot a 3-D dataset with a color variable as text labels.
points3D
is shorthand for scatter3D(..., type = "p")
lines3D
is shorthand for scatter3D(..., type = "l")
points2D
is shorthand for scatter2D(..., type = "p")
lines2D
is shorthand for scatter2D(..., type = "l")
The 2D functions are included for their side effect of having a color key.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | scatter3D (x, y, z, ..., colvar = z, phi = 40, theta = 40,
col = NULL, NAcol = "white", breaks = NULL,
colkey = NULL, panel.first = NULL,
clim = NULL, clab = NULL,
bty = "b", CI = NULL, surf = NULL,
add = FALSE, plot = TRUE)
text3D (x, y, z, labels, ..., colvar = NULL, phi = 40, theta = 40,
col = NULL, NAcol = "white", breaks = NULL,
colkey = NULL, panel.first = NULL,
clim = NULL, clab = NULL,
bty = "b", add = FALSE, plot = TRUE)
points3D (x, y, z, ...)
lines3D (x, y, z, ...)
scatter2D (x, y, ..., colvar = NULL,
col = NULL, NAcol = "white", breaks = NULL,
colkey = NULL, clim = NULL, clab = NULL,
CI = NULL, add = FALSE, plot = TRUE)
lines2D(x, y, ...)
points2D(x, y, ...)
text2D (x, y, labels, ..., colvar = NULL,
col = NULL, NAcol = "white", breaks = NULL, colkey = NULL,
clim = NULL, clab = NULL, add = FALSE, plot = TRUE)
|
x, y, z |
Vectors with x, y and z-values of the points to be plotted.
They should be of equal length, and the same length as |
colvar |
The variable used for coloring. For |
theta, phi |
the angles defining the viewing direction.
|
col |
Color palette to be used for coloring the |
NAcol |
Colors to be used for |
breaks |
a set of finite numeric breakpoints for the colors; must have one more breakpoint than color and be in increasing order. Unsorted vectors will be sorted, with a warning. |
colkey |
A logical, The default is to draw the color key on side = 4, i.e. in the right margin.
If |
CI |
A |
panel.first |
A |
clab |
Only if |
clim |
Only if |
bty |
The type of the box, the default draws only the back panels.
Only effective if the persp
argument ( |
labels |
The text to be written. A vector of length equal to length of x, y, z. |
surf |
If not |
add |
Logical. If |
plot |
Logical. If |
... |
additional arguments passed to the plotting methods. The following persp arguments can be specified:
In addition, the perspbox arguments
For all functions, the arguments In case The arguments after ... must be matched exactly. |
Function scatter3D
returns the viewing transformation matrix.
See trans3D.
For scatter2D
and scatter3D
the plottypes that are supported
are: type = "p"
, type = "l"
, type = "h"
,
type = "o"
. For type = "b"
, type = "o"
is used instead.
Karline Soetaert <karline.soetaert@nioz.nl>
persp for the function on which this implementation is based.
mesh, trans3D, slice3D
, for other examples of
scatter2D
or scatter3D
.
plotdev for zooming, rescaling, rotating a plot.
package scatterplot3D
for an implementation of scatterplots that is
not based on persp
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 | # save plotting parameters
pm <- par("mfrow")
## =======================================================================
## A sphere
## =======================================================================
par(mfrow = c(1, 1))
M <- mesh(seq(0, 2*pi, length.out = 100),
seq(0, pi, length.out = 100))
u <- M$x ; v <- M$y
x <- cos(u)*sin(v)
y <- sin(u)*sin(v)
z <- cos(v)
# full panels of box are drawn (bty = "f")
scatter3D(x, y, z, pch = ".", col = "red",
bty = "f", cex = 2, colkey = FALSE)
## =======================================================================
## Different types
## =======================================================================
par (mfrow = c(2, 2))
z <- seq(0, 10, 0.2)
x <- cos(z)
y <- sin(z)*z
# greyish background for the boxtype (bty = "g")
scatter3D(x, y, z, phi = 0, bty = "g",
pch = 20, cex = 2, ticktype = "detailed")
# add another point
scatter3D(x = 0, y = 0, z = 0, add = TRUE, colkey = FALSE,
pch = 18, cex = 3, col = "black")
# add text
text3D(x = cos(1:10), y = (sin(1:10)*(1:10) - 1),
z = 1:10, colkey = FALSE, add = TRUE,
labels = LETTERS[1:10], col = c("black", "red"))
# line plot
scatter3D(x, y, z, phi = 0, bty = "g", type = "l",
ticktype = "detailed", lwd = 4)
# points and lines
scatter3D(x, y, z, phi = 0, bty = "g", type = "b",
ticktype = "detailed", pch = 20,
cex = c(0.5, 1, 1.5))
# vertical lines
scatter3D(x, y, z, phi = 0, bty = "g", type = "h",
ticktype = "detailed")
## =======================================================================
## With confidence interval
## =======================================================================
x <- runif(20)
y <- runif(20)
z <- runif(20)
par(mfrow = c(1, 1))
CI <- list(z = matrix(nrow = length(x), ncol = 2,
data = rep(0.05, times = 2*length(x))))
# greyish background for the boxtype (bty = "g")
scatter3D(x, y, z, phi = 0, bty = "g", CI = CI,
col = gg.col(100), pch = 18, cex = 2, ticktype = "detailed",
xlim = c(0, 1), ylim = c(0, 1), zlim = c(0, 1))
# add new set of points
x <- runif(20)
y <- runif(20)
z <- runif(20)
CI2 <- list(x = matrix(nrow = length(x), ncol = 2,
data = rep(0.05, 2*length(x))),
z = matrix(nrow = length(x), ncol = 2,
data = rep(0.05, 2*length(x))))
scatter3D(x, y, z, CI = CI2, add = TRUE, col = "red", pch = 16)
## =======================================================================
## With a surface
## =======================================================================
par(mfrow = c(1, 1))
# surface = volcano
M <- mesh(1:nrow(volcano), 1:ncol(volcano))
# 100 points above volcano
N <- 100
xs <- runif(N) * 87
ys <- runif(N) * 61
zs <- runif(N)*50 + 154
# scatter + surface
scatter3D(xs, ys, zs, ticktype = "detailed", pch = 16,
bty = "f", xlim = c(1, 87), ylim = c(1,61), zlim = c(94, 215),
surf = list(x = M$x, y = M$y, z = volcano,
NAcol = "grey", shade = 0.1))
## =======================================================================
## A surface and CI
## =======================================================================
par(mfrow = c(1, 1))
M <- mesh(seq(0, 2*pi, length = 30), (1:30)/100)
z <- with (M, sin(x) + y)
# points 'sampled'
N <- 30
xs <- runif(N) * 2*pi
ys <- runif(N) * 0.3
zs <- sin(xs) + ys + rnorm(N)*0.3
CI <- list(z = matrix(nrow = length(xs),
data = rep(0.3, 2*length(xs))),
lwd = 3)
# facets = NA makes a transparent surface; borders are black
scatter3D(xs, ys, zs, ticktype = "detailed", pch = 16,
xlim = c(0, 2*pi), ylim = c(0, 0.3), zlim = c(-1.5, 1.5),
CI = CI, theta = 20, phi = 30, cex = 2,
surf = list(x = M$x, y = M$y, z = z, border = "black", facets = NA)
)
## =======================================================================
## droplines till the fitted surface
## =======================================================================
with (mtcars, {
# linear regression
fit <- lm(mpg ~ wt + disp)
# predict values on regular xy grid
wt.pred <- seq(1.5, 5.5, length.out = 30)
disp.pred <- seq(71, 472, length.out = 30)
xy <- expand.grid(wt = wt.pred,
disp = disp.pred)
mpg.pred <- matrix (nrow = 30, ncol = 30,
data = predict(fit, newdata = data.frame(xy),
interval = "prediction")[,1])
# fitted points for droplines to surface
fitpoints <- predict(fit)
scatter3D(z = mpg, x = wt, y = disp, pch = 18, cex = 2,
theta = 20, phi = 20, ticktype = "detailed",
xlab = "wt", ylab = "disp", zlab = "mpg",
surf = list(x = wt.pred, y = disp.pred, z = mpg.pred,
facets = NA, fit = fitpoints),
main = "mtcars")
})
## =======================================================================
## Two ways to make a scatter 3D of quakes data set
## =======================================================================
par(mfrow = c(1, 1))
# first way, use vertical spikes (type = "h")
with(quakes, scatter3D(x = long, y = lat, z = -depth, colvar = mag,
pch = 16, cex = 1.5, xlab = "longitude", ylab = "latitude",
zlab = "depth, km", clab = c("Richter","Magnitude"),
main = "Earthquakes off Fiji", ticktype = "detailed",
type = "h", theta = 10, d = 2,
colkey = list(length = 0.5, width = 0.5, cex.clab = 0.75))
)
# second way: add dots on bottom and left panel
# before the scatters are drawn,
# add small dots on basal plane and on the depth plane
panelfirst <- function(pmat) {
zmin <- min(-quakes$depth)
XY <- trans3D(quakes$long, quakes$lat,
z = rep(zmin, nrow(quakes)), pmat = pmat)
scatter2D(XY$x, XY$y, colvar = quakes$mag, pch = ".",
cex = 2, add = TRUE, colkey = FALSE)
xmin <- min(quakes$long)
XY <- trans3D(x = rep(xmin, nrow(quakes)), y = quakes$lat,
z = -quakes$depth, pmat = pmat)
scatter2D(XY$x, XY$y, colvar = quakes$mag, pch = ".",
cex = 2, add = TRUE, colkey = FALSE)
}
with(quakes, scatter3D(x = long, y = lat, z = -depth, colvar = mag,
pch = 16, cex = 1.5, xlab = "longitude", ylab = "latitude",
zlab = "depth, km", clab = c("Richter","Magnitude"),
main = "Earthquakes off Fiji", ticktype = "detailed",
panel.first = panelfirst, theta = 10, d = 2,
colkey = list(length = 0.5, width = 0.5, cex.clab = 0.75))
)
## =======================================================================
## text3D and scatter3D
## =======================================================================
with(USArrests, text3D(Murder, Assault, Rape,
colvar = UrbanPop, col = gg.col(100), theta = 60, phi = 20,
xlab = "Murder", ylab = "Assault", zlab = "Rape",
main = "USA arrests",
labels = rownames(USArrests), cex = 0.6,
bty = "g", ticktype = "detailed", d = 2,
clab = c("Urban","Pop"), adj = 0.5, font = 2))
with(USArrests, scatter3D(Murder, Assault, Rape - 1,
colvar = UrbanPop, col = gg.col(100),
type = "h", pch = ".", add = TRUE))
## =======================================================================
## zoom near origin
## =======================================================================
# display axis ranges
getplist()[c("xlim","ylim","zlim")]
# choose suitable ranges
plotdev(xlim = c(0, 10), ylim = c(40, 150),
zlim = c(7, 25))
## =======================================================================
## text3D to label x- and y axis
## =======================================================================
par(mfrow = c(1, 1))
hist3D (x = 1:5, y = 1:4, z = VADeaths,
bty = "g", phi = 20, theta = -60,
xlab = "", ylab = "", zlab = "", main = "VADeaths",
col = "#0072B2", border = "black", shade = 0.8,
ticktype = "detailed", space = 0.15, d = 2, cex.axis = 1e-9)
text3D(x = 1:5, y = rep(0.5, 5), z = rep(3, 5),
labels = rownames(VADeaths),
add = TRUE, adj = 0)
text3D(x = rep(1, 4), y = 1:4, z = rep(0, 4),
labels = colnames(VADeaths),
add = TRUE, adj = 1)
## =======================================================================
## Scatter2D; bty can also be set = to one of the perspbox alernatives
## =======================================================================
par(mfrow = c(2, 2))
x <- seq(0, 2*pi, length.out = 30)
scatter2D(x, sin(x), colvar = cos(x), pch = 16,
ylab = "sin", clab = "cos", cex = 1.5)
# other box types:
scatter2D(x, sin(x), colvar = cos(x), type = "l", lwd = 4, bty = "g")
scatter2D(x, sin(x), colvar = cos(x), type = "b", lwd = 2, bty = "b2")
# transparent colors and spikes
scatter2D(x, sin(x), colvar = cos(x), type = "h", lwd = 4, alpha = 0.5)
## =======================================================================
## mesh examples and scatter2D
## =======================================================================
par(mfrow = c(1, 2))
x <- seq(-1, 1, by = 0.1)
y <- seq(-2, 2, by = 0.2)
grid <- mesh(x, y)
z <- with(grid, cos(x) * sin(y))
image2D(z, x = x, y = y)
points(grid)
scatter2D(grid$x, grid$y, colvar = z, pch = 20, cex = 2)
## =======================================================================
## scatter plot with confidence intervals
## =======================================================================
par(mfrow = c(2, 2))
x <- sort(rnorm(10))
y <- runif(10)
cv <- sqrt(x^2 + y^2)
CI <- list(lwd = 2)
CI$x <- matrix (nrow = length(x), ncol = 2, data = rep(0.25, 2*length(x)))
scatter2D(x, y, colvar = cv, pch = 16, cex = 2, CI = CI)
scatter2D(x, y, colvar = cv, pch = 16, cex = 2, CI = CI, type = "b")
CI$y <- matrix (nrow = length(x), ncol = 2, data = rep(0.05, 2*length(x)))
CI$col <- "black"
scatter2D(x, y, colvar = cv, pch = 16, cex = 2, CI = CI)
CI$y[c(2,4,8,10), ] <- NA # Some points have no CI
CI$x[c(2,4,8,10), ] <- NA # Some points have no CI
CI$alen <- 0.02 # increase arrow head
scatter2D(x, y, colvar = cv, pch = 16, cex = 2, CI = CI)
## =======================================================================
## Scatter on an image
## =======================================================================
par(mfrow = c(1, 1))
# image of oxygen saturation
oxlim <- range(Oxsat$val[,,1], na.rm = TRUE)
image2D(z = Oxsat$val[,,1], x = Oxsat$lon, y = Oxsat$lat,
contour = TRUE,
xlab = "longitude", ylab = "latitude",
main = "Oxygen saturation", clim = oxlim, clab = "%")
# (imaginary) measurements at 5 sites
lon <- c( 11.2, 6.0, 0.9, -4, -8.8)
lat <- c(-19.7,-14.45,-9.1,-3.8, -1.5)
O2sat <- c( 90, 95, 92, 85, 100)
# add to image; use same zrange; avoid adding a color key
scatter2D(colvar = O2sat, x = lon, y = lat, clim = oxlim, pch = 16,
add = TRUE, cex = 2, colkey = FALSE)
## =======================================================================
## Scatter on a contourplot
## =======================================================================
par(mfrow = c(1, 1))
# room for colorkey by setting colkey = list(plot = FALSE)
# contour plot of the ocean's bathymetry
Depth <- Hypsometry$z
Depth[Depth > 0] <- NA
contour2D(z = Depth, x = Hypsometry$x, y = Hypsometry$y,
xlab = "longitude", ylab = "latitude",
col = "black", NAcol = "grey", levels = seq(-6000, 0, by = 2000),
main = "Oxygen saturation along ship track",
colkey = list(plot = FALSE))
# add data to image; with a color key
scatter2D(colvar = O2sat, x = lon, y = lat, pch = 16,
add = TRUE, cex = 2, clab = "%")
## =======================================================================
## scatter2D for time-series plots
## =======================================================================
# Plotting sunspot 'anomalies'
sunspot <- data.frame(year = time(sunspot.month),
anom = sunspot.month - mean(sunspot.month))
# long-term moving average of anomaly
ff <- 100
sunspot$ma <- filter(sunspot$anom, rep(1/ff, ff), sides = 2)
with (sunspot, lines2D(year, anom,
colvar = anom > 0,
col = c("pink", "lightblue"),
main = "sunspot anomaly", type = "h",
colkey = FALSE, las = 1, xlab = "year", ylab = ""))
lines2D(sunspot$year, sunspot$ma, add = TRUE)
# The same
#with (sunspot, plot(year, anom,
# col = c("pink", "lightblue")[(anom > 0) + 1],
# main = "sunspot", type = "h", las = 1))
# but this does not work due to NAs...
# lines(sunspot$year, sunspot$ma)
## =======================================================================
## text2D
## =======================================================================
with(USArrests, text2D(x = Murder, y = Assault + 5, colvar = Rape,
xlab = "Murder", ylab = "Assault", clab = "Rape",
main = "USA arrests", labels = rownames(USArrests), cex = 0.6,
adj = 0.5, font = 2))
with(USArrests, scatter2D(x = Murder, y = Assault, colvar = Rape,
pch = 16, add = TRUE, colkey = FALSE))
# reset plotting parameters
par(mfrow = pm)
|
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