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## =============================================================================
## 3-d representation using slices in x, y or z
## =============================================================================
# x, y, z vectors or arrays, colvar: array
addslice <- function(poly, x, y, z, colvar, xs = NULL,
ys = NULL, zs = NULL, plist,
col = NULL, NAcol = "white", breaks = NULL,
border = NA, facets = TRUE, lwd = 1, lty = 1,
clim = NULL, shadedot = NULL,
lighting = FALSE, alpha = NULL) {
if (! ispresent(colvar))
stop("'colvar' has to be defined and be an array of dimension 3")
# check dimensionality
DD <- dim(colvar)
if (length(DD) != 3)
stop("'colvar' has to be an array of dimension 3")
if (DD[1] != length(x))
stop("dimension of 'colvar' not compatible with length of 'x'")
if (DD[2] != length(y))
stop("dimension of 'colvar' not compatible with length of 'y'")
if (DD[3] != length(z))
stop("dimension of 'colvar' not compatible with length of 'z'")
crange <- diff(clim)
N <- length(col) -1
# Colors for NA values
if (any (is.na(colvar)) & ! is.null(NAcol) ) {
CC <- checkcolors(colvar, col, NAcol, clim)
clim <- CC$lim
col <- CC$col
colvar <- CC$colvar
}
# Function to add images on a plane as polygons
image.plane <- function(xs, ys, zs, paint = FALSE, i = 0) {
if (i == 1) # all xs are same
ix <- FindInterval(xs[1], x, all.inside = TRUE)
else
ix <- FindInterval(xs, x, all.inside = TRUE)
if (i == 2)
iy <- FindInterval(ys[1], y, all.inside = TRUE)
else
iy <- FindInterval(ys, y, all.inside = TRUE)
if (i == 3)
iz <- FindInterval(zs[1], z, all.inside = TRUE)
else
iz <- FindInterval(zs, z, all.inside = TRUE)
# colorvar
cv <- matrix(nrow = nrow(xs), ncol = ncol(xs), data = colvar[cbind(ix, iy, iz)])
# add polygon
poly <<- addimg(poly, xs, ys, zs, colvar = cv, plist = plist,
col = col, NAcol = NAcol, breaks = breaks,
border = border, facets = facets,
resfac = 1, clim = clim, lwd = lwd, lty = lty,
ltheta = shadedot$ltheta, lphi = shadedot$lphi,
shade = shadedot$shade, lighting = lighting, alpha = alpha)
} # end function imageplane
# Function to first create a plane and then draw an image on it
add.plane <- function(xs, ys, zs, i = 0) {
M <- mesh(xs, ys, zs)
image.plane (M$x[,,], M$y[,,], M$z[,,], i = i) # [,,] to make sure it is an array
} # end function addplane
if (any(diff(c( is.matrix(xs), is.matrix(ys), is.matrix(zs)))) != 0)
stop ("'xs', 'ys' and 'zs' should be a matrix if one of them is")
if (is.matrix(xs)) { # xs,.. are matrices defining the plane on which to plot
if (any (dim(xs) != dim(ys)))
stop("'xs' and 'ys' should have same dimension")
if (any (dim(xs) != dim(zs)))
stop("'xs' and 'zs' should have same dimension")
image.plane(xs, ys, zs, paint = TRUE)
} else { # xs, ys, zs define the positions in x, y, z on which to plot
if (! is.null(xs))
for (x.s in xs[!is.na(xs)])
add.plane(x.s, y, z, 1)
if (! is.null(ys))
for (y.s in ys[!is.na(ys)])
add.plane(x, y.s, z, 2)
if (! is.null(zs))
for (z.s in zs[!is.na(zs)])
add.plane(x, y, z.s, 3)
}
return(poly)
}
## =============================================================================
## main slice3D function
## =============================================================================
slice3D <- function(x, y, z, colvar, ...,
phi = 40, theta = 40,
xs = min(x),
ys = max(y),
zs = min(z),
col = NULL, NAcol = "white", breaks = NULL,
border = NA, facets = TRUE,
colkey = NULL, panel.first = NULL,
clim = NULL, clab = NULL, bty = "b",
lighting = FALSE, shade = NA, ltheta = -135, lphi = 0,
add = FALSE, plot = TRUE) {
plist <- initplist(add)
dot <- splitdotpersp(list(...), bty, lighting, x, y, z, plist = plist,
shade, lphi, ltheta, breaks = breaks)
if (is.null(col))
if (is.null(breaks))
col <- jet.col(100)
else
col <- jet.col(length(breaks)-1)
iscolkey <- is.colkey(colkey, col)
if (iscolkey)
colkey <- check.colkey(colkey)
breaks <- check.breaks(breaks, col)
if (! is.null(dot$alpha)) col <- setalpha(col, dot$alpha)
if (is.null(clim))
clim <- range(colvar, na.rm = TRUE)
if (dot$clog) {
colvar <- log(colvar)
clim <- log(clim)
}
if (is.null(plist)) {
do.call("perspbox", c(alist(x = range(x), y = range(y),
z = range(z, na.rm = TRUE),
phi = phi, theta = theta, plot = plot,
colkey = colkey, col = col), dot$persp))
plist <- getplist()
}
if (is.function(panel.first))
panel.first(plist$mat)
lwd <- ifelse(is.null(dot$points$lwd), 1, dot$points$lwd)
dot$points$lwd <- NULL
lty <- ifelse(is.null(dot$points$lty), 1, dot$points$lty)
dot$points$lty <- NULL
Poly <- addslice(NULL, x, y, z, colvar, xs = xs, ys = ys, zs = zs, plist = plist,
col = col, NAcol = NAcol, breaks = breaks,
border = border, facets = facets,
clim = clim, shadedot = dot$shade, lwd = lwd, lty = lty,
lighting = lighting, alpha = dot$alpha)
if (iscolkey)
plist <- plistcolkey(plist, colkey, col, clim, clab,
dot$clog, type = "slice3D", breaks = breaks)
plist <- plot_struct_3D(plist, poly = Poly, plot = plot)
setplist(plist)
invisible(plist$mat)
}
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