Composite plots  R Documentation 
S3 method plot.plist
and function plotdev
plot the plotting list
to the current device.
Changes can be made to the perspective view, to the lighting and shading,
or to make colors transparent.
getplist
and setplist
retrieve and store information in the plotting list.
selectplist
selects parts from the plotting list, based on a userdefined function.
getplist()
setplist(plist)
plotdev(...)
## S3 method for class 'plist'
plot(x, ...)
selectplist(plist, SS)
x , plist 
The plotting 
SS 
Function which tests points for inclusion in the plotting list.
It should take as argument three vectors (x, y, z) and return a vector of
equal length that is either 
... 
Additional arguments to change the view or coloration.
Supported arguments to change the view are :
Supported arguments to change the lighting, or coloration are :

All 3D functions from package plot3D
produce or update a plotting list
that is local to the package. One can access this plotting list via getplist
and setplist
. The list is used to plot when, in a 3D function, the argument
plot
is TRUE
or via function plotdev
.
When new 3D objects are added to a plot, using the add
argument of the
plotting functions, then everything except the axes, is redrawn on top of
what was already there. This means that several object will be drawn multiple times,
and this may clutter the output. This may not be visible on your screen, but
it may become apparent when exported. Use plotdev
to create clean figures, where
every object is drawn only once.
The plotting list
can contain the following items:
mat
, the viewing transformation matrix,
a 4 x 4 matrix suitable for projecting 3D coordinates
(x, y, z) into the 2D plane using homogeneous 4D coordinates (x,y,z,v).
It can be used to superimpose additional graphical elements on the 3D plot, by any function that is defined on persp.
It can also be used to add lines
, arrows
or
points
, using the function trans3D.
plt
, with original plt
parameters and the plt
parameters used for the main frame.
persp
, with settings for the perspective box.
xlim, ylim, zlim
, with ranges.
scalefac
, the scaling factors in x, y and z direction,
used e.g. for shading.
dot
other plotting parameters passed to persp
.
colkey
, numkey
, with settings for the color key(s).
poly, segm, pt, CIpt, labels, arr
the information for drawing
polygons, segments, points, points with confidence intervals, labels and arrows,
that are part of the plot.
For the item poly
the elements are:
x, y, z
: A matrix with typically 4 or 5 rows, the first rows defining the x, y or z
values of each polygon, the last row contains NA
(and which therefore terminates a polygon).
col
: a vector with the colors for the facets of each polygon.
lwd, lty, border
: a vector with the line widths, line type and colors for the border of each polygon.
(note in Rfunction polygon, passing a vector of line widths is not implemented;
therefore, only the first value of lwd
will be used for all polygons).
When plot.plist
is called, the projection depth is calculated and used to sort the
facets and function polygon
used to draw them.
Returns the updated plotting list.
Once a 3D plot has been generated, a new device can be opened and
plotdev
used to plot also on this device.
plotdev
and plot(getplist())
are the same.
In an extension package, plot3Drgl
, a similar function, plotrgl
,
plots the graphs to the device opened with rgl
. This allows interactive
zooming, rotating, etc...
Karline Soetaert <karline.soetaert@nioz.nl>
# save plotting parameters
pm < par("mfrow")
pmar < par("mar")
## ========================================================================
## The volcano
## ========================================================================
par(mfrow = c(2, 2), mar = c(2, 2, 2, 2))
# The volcano at lower resolution
x < seq(1, nrow(volcano), by = 2)
y < seq(1, ncol(volcano), by = 2)
V < volcano[x,y]
persp3D(z = V)
# rotate
plotdev(theta = 0)
# light and transparence
plotdev(lighting = TRUE, lphi = 90, alpha = 0.6)
# zoom
plotdev(xlim = c(0.2, 0.6), ylim = c(0.2, 0.6), phi = 60)
## ========================================================================
## Two spheres
## ========================================================================
par(mfrow = c(1, 1), mar = c(0, 0, 0, 0))
# create a sphere
M < mesh(seq(0, 2*pi, length.out = 30),
seq(0, pi, length.out = 30))
u < M$x ; v < M$y
x < cos(u)*sin(v)
y < sin(u)*sin(v)
z < cos(v)
surf3D(x = 2*x, y = 2*y, z = 2*z,
colvar = NULL, lighting = TRUE, #plot = FALSE,
facets = NA, col = "blue", lwd = 5)
surf3D(x, y, z, colvar = NULL, lighting = TRUE,
col = "red", add = TRUE)
names(getplist())
# plot with different view:
plotdev(phi = 0)
## Not run: # will plot same 3D graph to pdf
pdf(file = "save.pdf")
plotdev()
dev.off()
## End(Not run)
## ========================================================================
## Two spheres and two planes
## ========================================================================
par(mar = c(2, 2, 2, 2))
# equation of a sphere
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)
surf3D(x, y, z, colvar = z,
theta = 45, phi = 20, bty = "b",
xlim = c(1.5, 1.5), ylim = c(1, 2),
zlim = c(1.5, 1.5), plot = FALSE)
# add a second sphere, shifted 1 unit to the right on yaxis;
# no facets drawn for this sphere
surf3D (x, y+1, z, colvar = z, add = TRUE,
facets = FALSE, plot = FALSE)
# define a plane at z = 0
Nx < 100
Ny < 100
x < seq(1.5, 1.5, length.out = Nx)
y < seq(1, 2, length.out = Ny)
image3D (x = x, y = y, z = 0, add = TRUE, colvar = NULL,
col = "blue", facets = TRUE, plot = FALSE)
# another, small plane at y = 0  here x and y have to be matrices!
x < seq(1., 1., length.out = 50)
z < seq(1., 1., length.out = 50)
image3D (x = x, y = 0, z = z, colvar = NULL,
add = TRUE, col = NA, border = "blue",
facets = TRUE, plot = TRUE)
## Not run: # rotate
for (angle in seq(0, 360, by = 10))
plotdev(theta = angle)
## End(Not run)
## ========================================================================
## Zooming, rescaling, lighting,...
## ========================================================================
par(mfrow = c(2, 2))
# The volcano
x < seq(1, nrow(volcano), by = 2)
y < seq(1, ncol(volcano), by = 2)
V < volcano[x,y]
# plot the volcano
persp3D (x, y, z = V, colvar = V, theta = 10, phi = 20,
box = FALSE, scale = FALSE, expand = 0.3,
clim = range(V), plot = FALSE)
# add a plane (image) at z = 170; jetcolored, transparant: only border
image3D(x, y, z = 170, add = TRUE, clim = range(V),
colvar = V, facets = NA, plot = FALSE, colkey = FALSE)
# add a contour (image) at z = 170; jetcolored,
contour3D(x, y, z = 170, add = TRUE, clim = range(V),
colvar = V, plot = FALSE, colkey = FALSE)
# plot it 
plot(getplist()) # same as plotdev()
# plot but with different expansion
plotdev(expand = 1)
# other perspective, and shading
plotdev(d = 2, r = 10, shade = 0.3)
# zoom and rotate
plotdev(xlim = c(10, 30), ylim = c(20, 30), phi = 50)
## ========================================================================
## Using setplist
## ========================================================================
polygon3D(runif(3), runif(3), runif(3))
# retrieve plotting list
plist < getplist()
names(plist)
plist$poly
# change copy of plotting list
plist$poly$col < "red"
# update internal plotting list
setplist(plist)
# plot updated list
plotdev()
## ========================================================================
## Using selectplist
## ========================================================================
polygon3D(runif(10), runif(10), runif(10), col = "red",
alpha = 0.2, plot = FALSE, ticktype = "detailed",
xlim = c(0,1), ylim = c(0, 1), zlim = c(0, 1))
polygon3D(runif(10)*0.5, runif(10), runif(10), col = "yellow",
alpha = 0.2, plot = FALSE, add = TRUE)
polygon3D(runif(10)*0.5+0.5, runif(10), runif(10), col = "green",
alpha = 0.2, plot = FALSE, add = TRUE)
points3D(runif(10), runif(10), runif(10), col = "blue",
add = TRUE, plot = FALSE)
segments3D(x0 = runif(10), y0 = runif(10), z0 = runif(10),
x1 = runif(10), y1 = runif(10), z1 = runif(10),
colvar = 1:10, add = TRUE, lwd = 3)
# retrieve plotting list
plist < getplist()
# selection function
SS < function (x, y, z) {
sel < rep(TRUE, length.out = length(x))
sel[x < 0.5] < FALSE
return(sel)
}
# The whole polygon will be removed or kept.
plot(x = selectplist(plist, SS),
xlim = c(0, 1), ylim = c(0, 1), zlim = c(0, 1))
# restore plotting parameters
par(mfrow = pm)
par(mar = pmar)
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