# NOT RUN {
# 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)
# }
# NOT RUN {
# 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)
# }
# NOT RUN {
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()
# }
# NOT RUN {
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)
# }
# NOT RUN {
# use of creatisosurf
iso <- createisosurf(x, y, z, F, level = 2)
head(iso)
triangle3D(iso, col = "green", shade = 0.3)
# }
# NOT RUN {
# 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)
# }
# NOT RUN {
## =======================================================================
## 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)
# }
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