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@agstudy
Created December 11, 2013 10:42
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sactter.grid <- function (x, y = NULL, z = NULL, color = par("col"), pch = NULL,
main = NULL, sub = NULL, xlim = NULL, ylim = NULL, zlim = NULL,
xlab = NULL, ylab = NULL, zlab = NULL, scale.y = 1, angle = 40,
axis = TRUE, tick.marks = TRUE, label.tick.marks = TRUE,
x.ticklabs = NULL, y.ticklabs = NULL, z.ticklabs = NULL,
y.margin.add = 0, grid = TRUE, box = TRUE, lab = par("lab"),
lab.z = mean(lab[1:2]), type = "p", highlight.3d = FALSE,
mar = c(5, 3, 4, 3) + 0.1, bg = par("bg"), col.axis = par("col.axis"),
col.grid = "grey", col.lab = par("col.lab"), cex.symbols = par("cex"),
cex.axis = 0.8 * par("cex.axis"), cex.lab = par("cex.lab"),
font.axis = par("font.axis"), font.lab = par("font.lab"),
lty.axis = par("lty"), lty.grid = par("lty"), lty.hide = NULL,
lty.hplot = par("lty"), log = "", ...)
{
mem.par <- par(mar = mar)
x.scal <- y.scal <- z.scal <- 1
xlabel <- if (!missing(x))
deparse(substitute(x))
ylabel <- if (!missing(y))
deparse(substitute(y))
zlabel <- if (!missing(z))
deparse(substitute(z))
if (highlight.3d && !missing(color))
warning("color is ignored when highlight.3d = TRUE")
if (!is.null(d <- dim(x)) && (length(d) == 2) && (d[2] >=
4))
color <- x[, 4]
else if (is.list(x) && !is.null(x$color))
color <- x$color
xyz <- xyz.coords(x = x, y = y, z = z, xlab = xlabel, ylab = ylabel,
zlab = zlabel, log = log)
if (is.null(xlab)) {
xlab <- xyz$xlab
if (is.null(xlab))
xlab <- ""
}
if (is.null(ylab)) {
ylab <- xyz$ylab
if (is.null(ylab))
ylab <- ""
}
if (is.null(zlab)) {
zlab <- xyz$zlab
if (is.null(zlab))
zlab <- ""
}
if (length(color) == 1)
color <- rep(color, length(xyz$x))
else if (length(color) != length(xyz$x))
stop("length(color) ", "must be equal length(x) or 1")
angle <- (angle%%360)/90
yz.f <- scale.y * abs(if (angle < 1) angle else if (angle >
3) angle - 4 else 2 - angle)
yx.f <- scale.y * (if (angle < 2)
1 - angle
else angle - 3)
if (angle > 2) {
temp <- xyz$x
xyz$x <- xyz$y
xyz$y <- temp
temp <- xlab
xlab <- ylab
ylab <- temp
temp <- xlim
xlim <- ylim
ylim <- temp
}
angle.1 <- (1 < angle && angle < 2) || angle > 3
angle.2 <- 1 <= angle && angle <= 3
dat <- cbind(as.data.frame(xyz[c("x", "y", "z")]), col = color)
if (!is.null(xlim)) {
xlim <- range(xlim)
dat <- dat[xlim[1] <= dat$x & dat$x <= xlim[2], , drop = FALSE]
}
if (!is.null(ylim)) {
ylim <- range(ylim)
dat <- dat[ylim[1] <= dat$y & dat$y <= ylim[2], , drop = FALSE]
}
if (!is.null(zlim)) {
zlim <- range(zlim)
dat <- dat[zlim[1] <= dat$z & dat$z <= zlim[2], , drop = FALSE]
}
n <- nrow(dat)
if (n < 1)
stop("no data left within (x|y|z)lim")
y.range <- range(dat$y[is.finite(dat$y)])
if (type == "p" || type == "h") {
y.ord <- rev(order(dat$y))
dat <- dat[y.ord, ]
if (length(pch) > 1)
if (length(pch) != length(y.ord))
stop("length(pch) ", "must be equal length(x) or 1")
else pch <- pch[y.ord]
if (length(bg) > 1)
if (length(bg) != length(y.ord))
stop("length(bg) ", "must be equal length(x) or 1")
else bg <- bg[y.ord]
if (length(cex.symbols) > 1)
if (length(cex.symbols) != length(y.ord))
stop("length(cex.symbols) ", "must be equal length(x) or 1")
else cex.symbols <- cex.symbols[y.ord]
daty <- dat$y
daty[!is.finite(daty)] <- mean(daty[is.finite(daty)])
if (highlight.3d && !(all(diff(daty) == 0)))
dat$col <- rgb(red = seq(0, 1, length = n) * (y.range[2] -
daty)/diff(y.range), green = 0, blue = 0)
}
p.lab <- par("lab")
y.range <- range(dat$y[is.finite(dat$y)], ylim)
y.prty <- pretty(y.range, n = lab[2], min.n = max(1, min(0.5 *
lab[2], p.lab[2])))
y.scal <- round(diff(y.prty[1:2]), digits = 12)
y.add <- min(y.prty)
dat$y <- (dat$y - y.add)/y.scal
y.max <- (max(y.prty) - y.add)/y.scal
if (!is.null(ylim))
y.max <- max(y.max, ceiling((ylim[2] - y.add)/y.scal))
x.range <- range(dat$x[is.finite(dat$x)], xlim)
x.prty <- pretty(x.range, n = lab[1], min.n = max(1, min(0.5 *
lab[1], p.lab[1])))
x.scal <- round(diff(x.prty[1:2]), digits = 12)
dat$x <- dat$x/x.scal
x.range <- range(x.prty)/x.scal
x.max <- ceiling(x.range[2])
x.min <- floor(x.range[1])
if (!is.null(xlim)) {
x.max <- max(x.max, ceiling(xlim[2]/x.scal))
x.min <- min(x.min, floor(xlim[1]/x.scal))
}
x.range <- range(x.min, x.max)
z.range <- range(dat$z[is.finite(dat$z)], zlim)
z.prty <- pretty(z.range, n = lab.z, min.n = max(1, min(0.5 *
lab.z, p.lab[2])))
z.scal <- round(diff(z.prty[1:2]), digits = 12)
dat$z <- dat$z/z.scal
z.range <- range(z.prty)/z.scal
z.max <- ceiling(z.range[2])
z.min <- floor(z.range[1])
if (!is.null(zlim)) {
z.max <- max(z.max, ceiling(zlim[2]/z.scal))
z.min <- min(z.min, floor(zlim[1]/z.scal))
}
z.range <- range(z.min, z.max)
plot.new()
if (angle.2) {
x1 <- x.min + yx.f * y.max
x2 <- x.max
}
else {
x1 <- x.min
x2 <- x.max + yx.f * y.max
}
plot.window(c(x1, x2), c(z.min, z.max + yz.f * y.max))
temp <- strwidth(format(rev(y.prty))[1], cex = cex.axis/par("cex"))
if (angle.2)
x1 <- x1 - temp - y.margin.add
else x2 <- x2 + temp + y.margin.add
plot.window(c(x1, x2), c(z.min, z.max + yz.f * y.max))
if (angle > 2)
par(usr = par("usr")[c(2, 1, 3:4)])
usr <- par("usr")
title(main, sub, ...)
if ("xy" %in% grid || grid) {
i <- x.min:x.max
segments(i, z.min, i + (yx.f * y.max), yz.f * y.max +
z.min, col = col.grid, lty = lty.grid)
i <- 0:y.max
segments(x.min + (i * yx.f), i * yz.f + z.min, x.max +
(i * yx.f), i * yz.f + z.min, col = col.grid, lty = lty.grid)
}
if ("xz" %in% grid) {
i <- x.min:x.max
segments(i + (yx.f * y.max), yz.f * y.max + z.min,
i + (yx.f * y.max), yz.f * y.max + z.max,
col = col.grid, lty = lty.grid)
temp <- yx.f * y.max
temp1 <- yz.f * y.max
i <- z.min:z.max
segments(x.min + temp,temp1 + i,
x.max + temp,temp1 + i , col = col.grid, lty = lty.grid)
}
if ("yz" %in% grid) {
i <- 0:y.max
segments(x.min + (i * yx.f), i * yz.f + z.min,
x.min + (i * yx.f) ,i * yz.f + z.max,
col = col.grid, lty = lty.grid)
temp <- yx.f * y.max
temp1 <- yz.f * y.max
i <- z.min:z.max
segments(x.min + temp,temp1 + i,
x.min, i , col = col.grid, lty = lty.grid)
}
if (axis) {
xx <- if (angle.2)
c(x.min, x.max)
else c(x.max, x.min)
if (tick.marks) {
xtl <- (z.max - z.min) * (tcl <- -par("tcl"))/50
ztl <- (x.max - x.min) * tcl/50
mysegs <- function(x0, y0, x1, y1) segments(x0,
y0, x1, y1, col = col.axis, lty = lty.axis)
i.y <- 0:y.max
mysegs(yx.f * i.y - ztl + xx[1], yz.f * i.y + z.min,
yx.f * i.y + ztl + xx[1], yz.f * i.y + z.min)
i.x <- x.min:x.max
mysegs(i.x, -xtl + z.min, i.x, xtl + z.min)
i.z <- z.min:z.max
mysegs(-ztl + xx[2], i.z, ztl + xx[2], i.z)
if (label.tick.marks) {
las <- par("las")
mytext <- function(labels, side, at, ...) mtext(text = labels,
side = side, at = at, line = -0.5, col = col.lab,
cex = cex.axis, font = font.lab, ...)
if (is.null(x.ticklabs))
x.ticklabs <- format(i.x * x.scal)
mytext(x.ticklabs, side = 1, at = i.x)
if (is.null(z.ticklabs))
z.ticklabs <- format(i.z * z.scal)
mytext(z.ticklabs, side = if (angle.1)
4
else 2, at = i.z, adj = if (0 < las && las <
3)
1
else NA)
temp <- if (angle > 2)
rev(i.y)
else i.y
if (is.null(y.ticklabs))
y.ticklabs <- format(y.prty)
else if (angle > 2)
y.ticklabs <- rev(y.ticklabs)
text(i.y * yx.f + xx[1], i.y * yz.f + z.min,
y.ticklabs, pos = if (angle.1)
2
else 4, offset = 1, col = col.lab, cex = cex.axis/par("cex"),
font = font.lab)
}
}
mytext2 <- function(lab, side, line, at) mtext(lab,
side = side, line = line, at = at, col = col.lab,
cex = cex.lab, font = font.axis, las = 0)
lines(c(x.min, x.max), c(z.min, z.min), col = col.axis,
lty = lty.axis)
mytext2(xlab, 1, line = 1.5, at = mean(x.range))
lines(xx[1] + c(0, y.max * yx.f), c(z.min, y.max * yz.f +
z.min), col = col.axis, lty = lty.axis)
mytext2(ylab, if (angle.1)
2
else 4, line = 0.5, at = z.min + y.max * yz.f)
lines(xx[c(2, 2)], c(z.min, z.max), col = col.axis,
lty = lty.axis)
mytext2(zlab, if (angle.1)
4
else 2, line = 1.5, at = mean(z.range))
if (box) {
if (is.null(lty.hide))
lty.hide <- lty.axis
temp <- yx.f * y.max
temp1 <- yz.f * y.max
lines(c(x.min + temp, x.max + temp), c(z.min + temp1,
z.min + temp1), col = col.axis, lty = lty.hide)
lines(c(x.min + temp, x.max + temp), c(temp1 + z.max,
temp1 + z.max), col = col.axis, lty = lty.axis)
temp <- c(0, y.max * yx.f)
temp1 <- c(0, y.max * yz.f)
lines(temp + xx[2], temp1 + z.min, col = col.axis,
lty = lty.hide)
lines(temp + x.min, temp1 + z.max, col = col.axis,
lty = lty.axis)
temp <- yx.f * y.max
temp1 <- yz.f * y.max
lines(c(temp + x.min, temp + x.min), c(z.min + temp1,
z.max + temp1), col = col.axis, lty = if (!angle.2)
lty.hide
else lty.axis)
lines(c(x.max + temp, x.max + temp), c(z.min + temp1,
z.max + temp1), col = col.axis, lty = if (angle.2)
lty.hide
else lty.axis)
}
}
x <- dat$x + (dat$y * yx.f)
z <- dat$z + (dat$y * yz.f)
col <- as.character(dat$col)
if (type == "h") {
z2 <- dat$y * yz.f + z.min
segments(x, z, x, z2, col = col, cex = cex.symbols,
lty = lty.hplot, ...)
points(x, z, type = "p", col = col, pch = pch, bg = bg,
cex = cex.symbols, ...)
}
else points(x, z, type = type, col = col, pch = pch, bg = bg,
cex = cex.symbols, ...)
if (axis && box) {
lines(c(x.min, x.max), c(z.max, z.max), col = col.axis,
lty = lty.axis)
lines(c(0, y.max * yx.f) + x.max, c(0, y.max * yz.f) +
z.max, col = col.axis, lty = lty.axis)
lines(xx[c(1, 1)], c(z.min, z.max), col = col.axis,
lty = lty.axis)
}
ob <- ls()
rm(list = ob[!ob %in% c("angle", "mar", "usr", "x.scal",
"y.scal", "z.scal", "yx.f", "yz.f", "y.add", "z.min",
"z.max", "x.min", "x.max", "y.max", "x.prty", "y.prty",
"z.prty")])
rm(ob)
invisible(list(xyz.convert = function(x, y = NULL, z = NULL) {
xyz <- xyz.coords(x, y, z)
if (angle > 2) {
temp <- xyz$x
xyz$x <- xyz$y
xyz$y <- temp
}
y <- (xyz$y - y.add)/y.scal
return(list(x = xyz$x/x.scal + yx.f * y, y = xyz$z/z.scal +
yz.f * y))
}, points3d = function(x, y = NULL, z = NULL, type = "p",
...) {
xyz <- xyz.coords(x, y, z)
if (angle > 2) {
temp <- xyz$x
xyz$x <- xyz$y
xyz$y <- temp
}
y2 <- (xyz$y - y.add)/y.scal
x <- xyz$x/x.scal + yx.f * y2
y <- xyz$z/z.scal + yz.f * y2
mem.par <- par(mar = mar, usr = usr)
on.exit(par(mem.par))
if (type == "h") {
y2 <- z.min + yz.f * y2
segments(x, y, x, y2, ...)
points(x, y, type = "p", ...)
} else points(x, y, type = type, ...)
}, plane3d = function(Intercept, x.coef = NULL, y.coef = NULL,
lty = "dashed", lty.box = NULL, ...) {
if (!is.atomic(Intercept) && !is.null(coef(Intercept))) Intercept <- coef(Intercept)
if (is.null(lty.box)) lty.box <- lty
if (is.null(x.coef) && length(Intercept) == 3) {
x.coef <- Intercept[if (angle > 2) 3 else 2]
y.coef <- Intercept[if (angle > 2) 2 else 3]
Intercept <- Intercept[1]
}
mem.par <- par(mar = mar, usr = usr)
on.exit(par(mem.par))
x <- x.min:x.max
ltya <- c(lty.box, rep(lty, length(x) - 2), lty.box)
x.coef <- x.coef * x.scal
z1 <- (Intercept + x * x.coef + y.add * y.coef)/z.scal
z2 <- (Intercept + x * x.coef + (y.max * y.scal + y.add) *
y.coef)/z.scal
segments(x, z1, x + y.max * yx.f, z2 + yz.f * y.max,
lty = ltya, ...)
y <- 0:y.max
ltya <- c(lty.box, rep(lty, length(y) - 2), lty.box)
y.coef <- (y * y.scal + y.add) * y.coef
z1 <- (Intercept + x.min * x.coef + y.coef)/z.scal
z2 <- (Intercept + x.max * x.coef + y.coef)/z.scal
segments(x.min + y * yx.f, z1 + y * yz.f, x.max + y *
yx.f, z2 + y * yz.f, lty = ltya, ...)
}, box3d = function(...) {
mem.par <- par(mar = mar, usr = usr)
on.exit(par(mem.par))
lines(c(x.min, x.max), c(z.max, z.max), ...)
lines(c(0, y.max * yx.f) + x.max, c(0, y.max * yz.f) +
z.max, ...)
lines(c(0, y.max * yx.f) + x.min, c(0, y.max * yz.f) +
z.max, ...)
lines(c(x.max, x.max), c(z.min, z.max), ...)
lines(c(x.min, x.min), c(z.min, z.max), ...)
lines(c(x.min, x.max), c(z.min, z.min), ...)
}))
}
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