Last chance! 50% off unlimited learning
Sale ends in
slice3D plots a 3-D dataset with a color variable as slices or on surfaces.
slicecont3D plots a 3-D dataset with a color variable as contours on slices.
isosurf3D plots isosurfaces from a 3-D dataset.
voxel3D plots isosurfaces as scatterpoints.
createisosurf create the isosurfaces (triangulations)
from volumetric data. Its output can be plotted with triangle3D.
createvoxel creates voxels (x, y, z) points from volumetric data.
Its output can be plotted with scatter3D.
slice3D (x, y, z, colvar, ..., phi = 40, theta = 40,
xs = min(x), ys = max(y), zs = min(z),
col = NULL, NAcol = "white", breaks = NULL,
border = NA, facets = TRUE, colkey = NULL,
panel.first = NULL, clim = NULL,
clab = NULL, bty = "b",
lighting = FALSE, shade = NA, ltheta = -135, lphi = 0,
add = FALSE, plot = TRUE) slicecont3D (x, y, z, colvar, ..., phi = 40, theta = 40,
xs = NULL, ys = NULL, zs = NULL, level = NULL,
col = NULL, NAcol = "white", breaks = NULL,
border = NA, facets = TRUE,
colkey = NULL, panel.first = NULL,
clim = NULL, clab = NULL, bty = "b",
dDepth = 0, add = FALSE, plot = TRUE)
isosurf3D (x, y, z, colvar, ..., phi = 40, theta = 40,
level = mean(colvar, na.rm = TRUE), isofunc = createisosurf,
col = NULL, border = NA, facets = TRUE,
colkey = NULL, panel.first = NULL,
clab = NULL, bty = "b",
lighting = FALSE, shade = 0.5, ltheta = -135, lphi = 0,
add = FALSE, plot = TRUE)
voxel3D (x, y, z, colvar, ..., phi = 40, theta = 40,
level = mean(colvar, na.rm = TRUE), eps = 0.01, operator = "=",
col = NULL, NAcol = "white", breaks = NULL, colkey = FALSE,
panel.first = NULL, bty = "b", add = FALSE, plot = TRUE)
triangle3D (tri, colvar = NULL, ..., phi = 40, theta = 40,
col = NULL, NAcol = "white", breaks = NULL,
border = NA, facets = TRUE,
colkey = NULL, panel.first = NULL,
lighting = FALSE, shade = 0.5, ltheta = -135, lphi = 0,
clim = NULL, clab = NULL,
bty = "b", add = FALSE, plot = TRUE)
createisosurf (x, y, z, colvar, level = mean(colvar, na.rm = TRUE))
createvoxel (x, y, z, colvar, level = mean(colvar, na.rm = TRUE), eps = 0.01,
operator = "=")
The plotting functions return the viewing transformation matrix, See trans3D.
Function createisosurf returns a three-columned matrix (x, y, z) with
triangle coordinates. One triangle is defined by three consecutive rows.
It can be plotted with triangle3D.
Function createvoxel returns a list with the elements x, y, z
defining the points that are at a distance of less than
eps*diff(range(colvar)) from the required level.
Its output can be plotted with scatter3D.
Vectors with x, y and z-values.
They should be of length equal to the first, second and
third dimension of colvar respectively.
The variable used for coloring.
It should be an array of dimension equal to
c(length(x), length(y), length(z)).
For triangle3D, colvar should be of length = nrow(tri) / 3.
It must be present.
A three-columned matrix (x, y, z) with triangle coordinates. A triangle is defined by three consecutive rows.
A function defined as function(x, y, z, colvar, level),
and that returns the three-columned matrix with triangle coordinates.
The default, createisosurf uses function computeContour3d
from package misc3d.
the angles defining the viewing direction.
theta gives the azimuthal direction and phi the colatitude. see persp.
Colors to be used for coloring the colvar variable.
If col is NULL
then a red-yellow-blue colorscheme (jet.col) will be used.
Colors to be used for colvar values that are NA.
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.
The color of the lines drawn around the surface facets.
The default, NA, will disable the drawing of borders.
If TRUE, then col denotes the color of the surface facets.
If FALSE, then the surface facets are colored ``white'' and the border
(if NA) will be colored as specified by col.
If NA then the facets will be transparent.
It is usually faster to draw with facets = FALSE.
A logical, NULL (default), or a list with parameters
for the color key (legend). List parameters should be one of
side, plot, length, width, dist, shift, addlines, col.clab, cex.clab,
side.clab, line.clab, adj.clab, font.clab
and the axis parameters at, labels, tick, line, pos, outer, font, lty, lwd,
lwd.ticks, col.box, col.axis, col.ticks, hadj, padj, cex.axis, mgp, tck, tcl, las.
The defaults for the parameters are side = 4, plot = TRUE, length = 1, width = 1,
dist = 0, shift = 0, addlines = FALSE, col.clab = NULL, cex.clab = par("cex.lab"),
side.clab = NULL, line.clab = NULL, adj.clab = NULL, font.clab = NULL)
See colkey.
The default is to draw the color key on side = 4, i.e. in the right margin.
If colkey = NULL then a color key will be added only if col is a vector.
Setting colkey = list(plot = FALSE) will create room for the color key
without drawing it.
if colkey = FALSE, no color key legend will be added.
A function to be evaluated after the plot axes are
set up but before any plotting takes place.
This can be useful for drawing background grids or scatterplot smooths.
The function should have as argument the transformation matrix, e.g. it should
be defined as function(pmat). See last example and example of persp3D.
Only if colkey is not NULL or FALSE,
the label to be written on top of the color key.
The label will be written at the same level as the main title.
To lower it, clab can be made a vector, with the first values empty
strings.
Only if colvar is specified, the range of the color variable, used
for the color key. Values of colvar that extend the range will be put to NA.
Vectors or matrices.
Vectors specify the positions in x, y or z where the slices (planes) are to be drawn.
The values of colvar will be projected on these slices.
Matrices specify a surface on which the colvar will be projected.
The level(s) at which the contour will be generated or the
isosurfaces generated.
There can be more than one level, but for slicecont3D too many
will give a crowded view, and one is often best.
For isosurf3D, the use of multiple values may need transparent colors to visualise.
For voxel3D, level should either be one number (if operator
equals '=', '<', '>') or two numbers (for operator = '<>').
If not FALSE the facets will be illuminated, and colors may
appear more bright. To switch on lighting, the argument lighting
should be either set to TRUE (using default settings) or it can be a
list with specifications of one of the following:
ambient, diffuse, specular, exponent, sr and alpha.
Will overrule shade not equal to NA.
See examples in jet.col.
the degree of shading of the surface facets. Values of shade close to one yield shading similar to a point light source model and values close to zero produce no shading. Values in the range 0.5 to 0.75 provide an approximation to daylight illumination. See persp.
if finite values are specified for ltheta and
lphi, the surface is shaded as though it was being illuminated from
the direction specified by azimuth ltheta and colatitude lphi.
See persp.
The type of the box, the default only draws background panels.
Only effective if the persp
argument (box) equals TRUE (this is the default). See perspbox.
The voxel precision, only used when operator = "=".
A point is selected if it closer than eps*diff(range(colvar))
to the required level.
One of '=', '<', '>', '<>' for selection of points `equal' (within precision), larger or smaller than the required level or to be within an interval.
When a contour is added on an image, the image polygons may
hide some contour segments. To avoid that, the viewing depth of the segments
can be artificially decreased with the factor dDepth times the
persp argument expand (usually = 1), to make them
appear in front of the polygons.
Too large values of dDepth may create visible artifacts.
See contour3D.
Logical. If TRUE, then the slices, voxels or surfaces will be added to the current plot.
If FALSE a new plot is started.
Logical. If TRUE (default), a plot is created,
otherwise the viewing transformation matrix is returned (as invisible).
additional arguments passed to the plotting methods.
The following persp arguments can be specified:
xlim, ylim, zlim, xlab, ylab, zlab, main, sub, r, d,
scale, expand, box, axes, nticks, ticktype.
The arguments xlim, ylim, zlim only affect the axes.
All objects will be plotted, including those that fall out of these ranges.
To select objects only within the axis limits, use plotdev.
In addition, the perspbox arguments
col.axis, col.panel, lwd.panel, col.grid, lwd.grid can
also be given a value.
alpha can be given a value inbetween 0 and 1 to make colors transparent.
For all functions, the arguments lty, lwd can be specified.
The arguments after ... must be matched exactly.
Karline Soetaert <karline.soetaert@nioz.nl>
Lorensen, W.E. and Cline, H.E., Marching Cubes: a high resolution 3D surface reconstruction algorithm, Computer Graphics, Vol. 21, No. 4, pp 163-169 (Proc. of SIGGRAPH), 1987.
Dai Feng, Luke Tierney, Computing and Displaying Isosurfaces in R, Journal of Statistical Software 28(1), 2008. URL https://www.jstatsoft.org/v28/i01/.
Oxsat for another example of slice3D.
plotdev for zooming, rescaling, rotating a plot.
# save plotting parameters
pm <- par("mfrow")
pmar <- par("mar")
## =======================================================================
## Simple slice3D examples
## =======================================================================
par(mfrow = c(2, 2))
x <- y <- z <- seq(-1, 1, by = 0.1)
grid <- mesh(x, y, z)
colvar <- with(grid, x*exp(-x^2 - y^2 - z^2))
# default is just the panels
slice3D (x, y, z, colvar = colvar, theta = 60)
# contour slices
slicecont3D (x, y, z, ys = seq(-1, 1, by = 0.5), colvar = colvar,
theta = 60, border = "black")
slice3D (x, y, z, xs = c(-1, -0.5, 0.5), ys = c(-1, 0, 1),
zs = c(-1, 0), colvar = colvar,
theta = 60, phi = 40)
## =======================================================================
## coloring on a surface
## =======================================================================
XY <- mesh(x, y)
ZZ <- XY$x*XY$y
slice3D (x, y, z, xs = XY$x, ys = XY$y, zs = ZZ, colvar = colvar,
lighting = TRUE, lphi = 90, ltheta = 0)
## =======================================================================
## Specifying transparent colors
## =======================================================================
par(mfrow = c(1, 1))
x <- y <- z <- seq(-4, 4, by = 0.2)
M <- mesh(x, y, z)
R <- with (M, sqrt(x^2 + y^2 + z^2))
p <- sin(2*R) /(R+1e-3)
if (FALSE) {
# This is very slow - alpha = 0.5 makes it transparent
slice3D(x, y, z, colvar = p, col = jet.col(alpha = 0.5),
xs = 0, ys = c(-4, 0, 4), zs = NULL, d = 2)
}
slice3D(x, y, z, colvar = p, d = 2, theta = 60, border = "black",
xs = c(-4, 0), ys = c(-4, 0, 4), zs = c(-4, 0))
## =======================================================================
## A section along a transect
## =======================================================================
data(Oxsat)
Ox <- Oxsat$val[, Oxsat$lat > - 5 & Oxsat$lat < 5, ]
slice3D(x = Oxsat$lon, z = -Oxsat$depth, y = 1:5, colvar = Ox,
ys = 1:5, zs = NULL, NAcol = "black",
expand = 0.4, theta = 45, phi = 45)
## =======================================================================
## isosurf3D example - rather slow
## =======================================================================
par(mfrow = c(2, 2), mar = c(2, 2, 2, 2))
x <- y <- z <- seq(-2, 2, length.out = 15)
xyz <- mesh(x, y, z)
F <- with(xyz, log(x^2 + y^2 + z^2 +
10*(x^2 + y^2) * (y^2 + z^2) ^2))
# use shading for level = 1 - show triangulation with border
isosurf3D(x, y, z, F, level = 1, shade = 0.9,
col = "yellow", border = "orange")
# lighting for level - 2
isosurf3D(x, y, z, F, level = 2, lighting = TRUE,
lphi = 0, ltheta = 0, col = "blue", shade = NA)
# three levels, transparency added
isosurf3D(x, y, z, F, level = seq(0, 4, by = 2),
col = c("red", "blue", "yellow"),
clab = "F", alpha = 0.2, theta = 0, lighting = TRUE)
# transparency can also be added afterwards with plotdev()
if (FALSE) {
isosurf3D(x, y, z, F, level = seq(0, 4, by = 2),
col = c("red", "blue", "yellow"),
shade = NA, plot = FALSE, clab = "F")
plotdev(lighting = TRUE, alpha = 0.2, theta = 0)
}
# use of creatisosurf
iso <- createisosurf(x, y, z, F, level = 2)
head(iso)
triangle3D(iso, col = "green", shade = 0.3)
if (FALSE) {
# higher resolution
x <- y <- z <- seq(-2, 2, length.out = 50)
xyz <- mesh(x, y, z)
F <- with(xyz, log(x^2 + y^2 + z^2 +
10*(x^2 + y^2) * (y^2 + z^2) ^2))
# three levels
isosurf3D(x, y, z, F, level = seq(0, 4, by = 2),
col = c("red", "blue", "yellow"),
shade = NA, plot = FALSE, clab = "F")
plotdev(lighting = TRUE, alpha = 0.2, theta = 0)
}
## =======================================================================
## voxel3D example
## =======================================================================
par(mfrow = c(2, 2), mar = c(2, 2, 2, 2))
# fast but needs high resolution grid
x <- y <- z <- seq(-2, 2, length.out = 70)
xyz <- mesh(x, y, z)
F <- with(xyz, log(x^2 + y^2 + z^2 +
10*(x^2 + y^2) * (y^2 + z^2) ^2))
voxel3D(x, y, z, F, level = 4, pch = ".", cex = 5)
## =======================================================================
## rotation
## =======================================================================
plotdev(theta = 45, phi = 0)
plotdev(theta = 90, phi = 10)
# same using createvoxel - more flexible for coloring
vox <- createvoxel(x, y, z, F, level = 4)
scatter3D(vox$x, vox$y, vox$z, colvar = vox$y,
bty = "g", colkey = FALSE)
## =======================================================================
## voxel3D to show hypox sites
## =======================================================================
par(mfrow = c(1, 1), mar = c(2, 2, 2, 2))
Hypox <- createvoxel(Oxsat$lon, Oxsat$lat, Oxsat$depth[1:19],
Oxsat$val[,,1:19], level = 40, operator = "<")
panel <- function(pmat) { # an image at the bottom
Nx <- length(Oxsat$lon)
Ny <- length(Oxsat$lat)
M <- mesh(Oxsat$lon, Oxsat$lat)
xy <- trans3D(pmat = pmat, x = as.vector(M$x), y = as.vector(M$y),
z = rep(-1000, length.out = Nx*Ny))
x <- matrix(nrow = Nx, ncol = Ny, data = xy$x)
y <- matrix(nrow = Nx, ncol = Ny, data = xy$y)
Bat <- Oxsat$val[,,1]; Bat[!is.na(Bat)] <- 1
image2D(x = x, y = y, z = Bat, NAcol = "black", col = "grey",
add = TRUE, colkey = FALSE)
}
scatter3D(Hypox$x, Hypox$y, -Hypox$z, colvar = Hypox$cv,
panel.first = panel, pch = ".", bty = "b",
theta = 30, phi = 20, ticktype = "detailed",
zlim = c(-1000,0), xlim = range(Oxsat$lon),
ylim = range(Oxsat$lat) )
# restore plotting parameters
par(mfrow = pm)
par(mar = pmar)
Run the code above in your browser using DataLab