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# a function to create polygons from vectors
add.poly <- function(poly, x, y, z, cv, col, NAcol, breaks,
clim, facets, border, lwd = 1, lty = 1, ...) {
nr <- nrow(x) - 1
nc <- ncol(x) - 1
# create polygons
ix <- rep(1:nr, nc)
iy <- as.vector(matrix(nrow = nr, ncol = nc,
data = 1:nc, byrow =TRUE))
xx <- x
yy <- y
zz <- z
# the polygon coordinates
PolyX <- rbind(xx[cbind(ix, iy )],
xx[cbind(ix + 1, iy )],
xx[cbind(ix + 1, iy + 1)],
xx[cbind(ix, iy + 1)], NA)
PolyY <- rbind(yy[cbind(ix, iy )],
yy[cbind(ix + 1, iy )],
yy[cbind(ix + 1, iy + 1)],
yy[cbind(ix, iy + 1)], NA)
PolyZ <- rbind(zz[cbind(ix, iy )],
zz[cbind(ix + 1, iy )],
zz[cbind(ix + 1, iy + 1)],
zz[cbind(ix, iy + 1)], NA)
# colvar is converted to colors.
if (! is.null(cv)) {
if (length(cv) == nrow(x)) # take colvar averages
cv <- 0.5*(cv[-1] + cv[-length(cv)])
# Colors for values = NA
if (any (is.na(cv)) & ! is.null(NAcol) ) {
CC <- checkcolors(cv, col, NAcol, clim)
clim <- CC$lim
col <- CC$col
cv <- CC$colvar
}
if (is.null(breaks)) {
crange <- diff(clim)
N <- length(col) -1
Col <- col[1 + trunc((cv - clim[1])/crange*N)]
} else {
zi <- .bincode(cv, breaks, TRUE, TRUE)
Col <- col[zi]
Col[is.na(Col)] <- NAcol
}
} else
Col <- rep(col, length.out = length(cv))
Lty <- rep(lty, length.out = length(cv))
Lwd <- rep(lwd, length.out = length(cv))
# border and colors
Col <- createcolors(facets, border, Col)
# update polygons.
poly <-
list(x = cbind(poly$x, PolyX),
y = cbind(poly$y, PolyY),
z = cbind(poly$z, PolyZ),
col = c(poly$col, Col$facet),
border = c(poly$border, Col$border),
lty = c(poly$lty, Lty),
lwd = c(poly$lwd, Lwd),
isimg = c(poly$isimg, rep(0, length.out = length(cv))),
img = poly$img
)
return(poly)
}
## =============================================================================
## Adding polygons from images or persps
## =============================================================================
addimg <- function(poly, x, y, z, colvar = z, plist,
col = NULL, NAcol = "white", breaks = NULL,
border = NA, facets = TRUE, lwd = 1, lty = 1,
resfac = 1, clim = NULL,
ltheta = -135, lphi = 0, shade = NA,
lighting = FALSE, alpha = NULL, ...) {
if (missing(poly) | is.null(poly) | length(poly) == 0)
poly <- list(x = NULL, y = NULL, col = NULL, border = NULL,
lwd = NULL, lty = NULL, proj = NULL, isimg = NULL,
img = list())
else if (!inherits(poly, "poly"))
stop ("'poly' not of correct type for addimg")
dot <- splitdotpersp(list(),
bty = NULL, lighting, x, y, z, plist = plist,
ltheta = ltheta, lphi = lphi, shade = shade, breaks = breaks)
if (! is.null(plist$xs)) {
dot$shade$xs <- plist$scalefac$x
dot$shade$ys <- plist$scalefac$y
dot$shade$zs <- plist$scalefac$z
}
if (! is.matrix(z))
stop("'z' should be a matrix")
if (! is.null(colvar)) {
if (! is.matrix(colvar))
stop("'colvar' should be a matrix or NULL")
if (any (dim(z) != dim(colvar)) )
stop("dimension of 'colvar' not equal to dimension of 'z'")
if (is.null(col))
col <- jet.col(100)
}
if (is.null(col))
col <- "grey"
# if x and y are a vector: check resfac and convert to matrix
X <- x
Y <- y
if (is.vector(X)) {
if (! is.vector(Y))
stop("'y' should be a vector if 'x' is one")
if (any(resfac != 1)) { # change resolution
res <- changeres(resfac, X, Y, z, colvar)
X <- res$x
Y <- res$y
z <- res$z
colvar <- res$colvar
}
XY <- mesh(X, Y)
x <- XY$x
y <- XY$y
} else {
x <- X
y <- Y
}
# check class and dimensionality
if (! is.matrix(x))
stop("'x' should be a matrix or vector")
if (! is.matrix(y))
stop("'y' should be a matrix or vector")
DD <- dim(x)
if (any (DD != dim(y)) )
stop("dimension of 'x' not equal to dimension of 'y'")
if (any (DD != dim(z)) )
stop("dimension of 'y' not equal to dimension of 'z'")
# create polygons - unsorted
ix <- rep(1:nrow(x), ncol(x))
iy <- as.vector(matrix(nrow = nrow(x), ncol = ncol(x),
data = 1:ncol(x), byrow =TRUE))
Poly <- createpoly(x, y, z, ix, iy)
# depth view of the points
Proj <- project(colMeans(Poly$X, na.rm = TRUE),
colMeans(Poly$Y, na.rm = TRUE),
colMeans(Poly$Z, na.rm = TRUE), plist)
# colvar is converted to colors.
if (! is.null(colvar)) {
if (is.null(clim))
clim <- range(colvar, na.rm = TRUE)
# Colors for values = NA
if (any (is.na(colvar)) & ! is.null(NAcol) ) {
CC <- checkcolors(colvar, col, NAcol, clim)
clim <- CC$lim
col <- CC$col
colvar <- CC$colvar
}
if (is.null(breaks)) {
crange <- diff(clim)
N <- length(col) -1
Col <- col[1 + trunc((colvar - clim[1])/crange*N)]
} else {
zi <- .bincode(colvar, breaks, TRUE, TRUE)
Col <- col[zi]
}
} else
Col <- rep(col, length.out = length(x))
Col[is.na(Col)] <- NAcol
if (! dot$shade$type == "none")
Col <- facetcols (x, y, z, Col, dot$shade)
if (! is.null(alpha))
Col <- setalpha(Col, alpha)
imgCol <- createcolors(facets, border, Col)
if (is.null(alpha)) alpha <- NA
Alpha <- alpha
alpha <- rep(alpha, length.out = length(x))
# update polygons.
numimg <- length(poly$img)
poly <-
list(x = cbind(poly$x, Poly$X),
y = cbind(poly$y, Poly$Y),
z = cbind(poly$z, Poly$Z),
col = c(poly$col, imgCol$facet),
border = c(poly$border, imgCol$border),
lwd = c(poly$lwd, rep(lwd , length.out = length(x))),
lty = c(poly$lty, rep(lty , length.out = length(x))),
proj = c(poly$proj, Proj),
isimg = c(poly$isimg, rep(1, length.out = length(x))),
alpha = c(poly$alpha, alpha),
img = poly$img)
if (numimg == 0)
poly$img <- list()
sl <- list (ix = ix, iy = iy, Proj = Proj, list = 1:length(ix))
poly$img[[numimg+1]] <- list(x = X, y = Y, z = z,
col = matrix(nrow = nrow(colvar),
ncol = ncol(colvar), data = Col), NAcol = NAcol,
breaks = breaks, sl = sl,
facets = facets, border = border, lwd = lwd, lty = lty,
alpha = Alpha, mapped = TRUE)
class(poly) <- "poly"
return(poly)
}
## =============================================================================
## Adds lines to segments
## =============================================================================
addlines <- function(segm, x, y, z, plist,
col, NAcol = "white",
lwd = 1, lty = 1,
ltheta = -135, lphi = 0, shade = NA,
lighting = FALSE, ignorez = TRUE, ...)
{
if (missing(segm) | is.null(segm))
segm <- list(x.from = NULL, x.to = NULL,
y.from = NULL, y.to = NULL,
z.from = NULL, z.to = NULL,
col = NULL, lwd = NULL, lty = NULL, proj = NULL)
else if (! inherits(segm, "segments"))
stop ("'segm' not of correct type, 'segments', for addlines")
dot <- splitdotpersp(list(),
bty = NULL, lighting, x, y, z, plist = plist,
ltheta = ltheta, lphi = lphi, shade = shade, breaks = NULL)
if (is.null(col))
col <- "black"
# check class and dimensionality
if (! is.vector(x))
stop("'x' should be a vector")
if (! is.vector(y))
stop("'y' should be a vector")
if (! is.vector(z))
stop("'z' should be a vector")
len <- length(x)
if (len != length(y) )
stop("dimension of 'x' not equal to dimension of 'y'")
if (len != length(z) )
stop("dimension of 'x' not equal to dimension of 'z'")
# depth view of the midpoints of each segment
Proj <- project(0.5*(x[-1] +x[-len]), 0.5*(y[-1]+y[-len]),
0.5*(z[-1]+z[-len]), plist, ignorez = ignorez)
Col <- rep(col, length.out = len-1)
if (! dot$shade$type == "none")
Col <- facetcols (x, y, z, Col, dot$shade)
alpha <- dot$alpha; if (is.null(alpha)) alpha <- NA
alpha <- rep(alpha, length.out = len-1)
# update and return segments.
segm <- list(
x.from = c(segm$x.from, x[-len]),
x.to = c(segm$x.to, x[-1]),
y.from = c(segm$y.from, y[-len]),
y.to = c(segm$y.to, y[-1]),
z.from = c(segm$z.from, z[-len]),
z.to = c(segm$z.to, z[-1]),
col = c(segm$col, Col),
lwd = c(segm$lwd, rep(lwd , length.out = len-1)),
lty = c(segm$lty, rep(lty , length.out = len-1)),
alpha = c(segm$alpha, alpha),
proj = c(segm$proj, Proj))
class(segm) <- "segments"
return(segm)
}
## =============================================================================
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