#########################################################################/**
# @RdocDefault points3d
#
# @title "Adding data points to a three dimensional plot"
#
# \description{
# Adding data points to a three dimensional plot previously created by
# \code{plot3d()} or \code{persp()}.
# Note that adding data points to a three dimensional plot will violate
# the depth order of the data points; data points that should be in the
# back, maybe hidden by other data points, might be plotted on top of
# the latter instead. Normally this behavior is not wanted and it is
# preferred to plot all data points at once using \code{plot3d()},
# which preserved the depth order.
# }
#
# @synopsis
#
# \arguments{
# \item{x}{the coordinates of points in the plot. Alternatively, a single
# plotting structure, function or any R object with a plot method can be
# provided.}
# \item{y}{the y coordinates of points in the plot, \emph{optional} if
# \code{x} is an appropriate structure.}
# \item{z}{the z coordinates of points in the plot, \emph{optional} if
# \code{x} is an appropriate structure.}
# \item{persp.matrix}{an 4-by-4 transformation matrix describing how
# to project the (x,y,z) points to the drawing canvas as the one
# returned by \code{persp}(). Default value is
# \code{getOption("persp.matrix")}, which is set by \code{plot3d()}.}
# \item{cex}{the character expansion of the data points. Default is
# \code{par("cex")}.}
# \item{col}{the color of the data points.
# Default value is \code{par("col")}.}
# \item{pch}{plotting "character", i.e. symbol to use. For more
# information see @see "graphics::points".
# Default value is \code{par("pch")}.}
# \item{depthOrder}{If @TRUE, the data points are plotted
# back-to-from relative to the view plane, otherwise they are plotted
# in the order they occur in the data.}
# \item{...}{further arguments accepted by @see "graphics::points".}
# }
#
# @author
#
# @examples "../incl/points3d.Rex"
#
# \seealso{
# For creating a 3D plot see @see "plot3d".
# For adding lines to a 3D plot see @see "lines3d".
# For adding text to a 3D plot see @see "text3d".
# For adding polygons to a 3D plot see @see "polygon3d".
# For adding stems to a 3D plot see @see "stem3d".
# See also @see "graphics::persp".
# Package \code{scatterplot3d} by Uwe Ligges.
# For detail about the graphical parameter arguments, see
# @see "graphics::par".
# }
#
# @keyword "aplot"
#*/#########################################################################
setMethodS3("points3d", "default", function(x=seq(0, 1, len=nrow(z)), y=seq(0, 1, len=ncol(z)), z, persp.matrix=getOption("persp.matrix"), cex=par("cex"), col=par("col"), pch=par("pch"), depthOrder=TRUE, ...) {
# Assert that the 4-by-4 perspective transform matrix is available
if (is.null(persp.matrix))
stop("Argument persp.matrix must be specified");
if (!is.matrix(persp.matrix) ||
nrow(persp.matrix) != 4 || ncol(persp.matrix) != 4) {
stop("Argument persp.matrix must be a 4x4 matrix as returned by for instance persp() or plot3d().");
}
# Extract the (x,y,z) coordinates
if (missing(z)) {
if (!missing(x)) {
if (is.list(x)) {
z <- x$z;
y <- x$y;
x <- x$x;
} else if (is.matrix(x)) {
z <- x[,3];
y <- x[,2];
x <- x[,1];
} else {
z <- x;
x <- seq(0, 1, len=nrow(z));
}
} else
stop("no `z' matrix specified");
} else if (is.list(x)) {
y <- x$y;
x <- x$x;
}
# Ben Bolker's function for projecting (x,y,z) to (x',y')
trans3d <- function(x,y,z,pmat) {
tmat <- t((cbind(x,y,z,1)%*% pmat))
list(x=tmat[1,]/tmat[4,], y=tmat[2,]/tmat[4,], z=tmat[3,]/tmat[4,])
}
# Transform the (x,y,z) in R^3 to (x',y') in R^2
xyz3d <- trans3d(x,y,z, persp.matrix);
# Should the points in the back be plotted first?
if (depthOrder) {
# Extract the depth order to make sure points at the back are plotted
# first
o <- order(xyz3d$z);
x <- xyz3d$x[o];
y <- xyz3d$y[o];
# Note that these parameters has to be included so they are also
# reordered by the depth.
n <- length(x);
if (!is.null(cex)) cex <- rep(cex, length.out=n)[o];
if (!is.null(col)) col <- rep(col, length.out=n)[o];
if (!is.null(pch)) pch <- rep(pch, length.out=n)[o];
} else {
x <- xyz3d$x;
y <- xyz3d$y;
n <- length(x);
if (!is.null(cex)) cex <- rep(cex, length.out=n);
if (!is.null(col)) col <- rep(col, length.out=n);
if (!is.null(pch)) pch <- rep(pch, length.out=n);
}
points(x,y, cex=cex, col=col, pch=pch, ...);
})
############################################################################
# HISTORY:
# 2005-02-20
# o Now using setMethodS3().
# 2003-07-07
# o Updated the Rdoc comments.
# 2003-03-08 - LAX airport
# o Made function also accept a matrix containing the xyz columns.
# o Made points3d() a generic function.
# 2003-03-03
# o BUG FIX: depthOrder=TRUE for points3d() messed up the order of the
# arguments cex, col and pch. This bug was introduced in previous update.
# 2003-01-05
# o Added argument depthOrder=TRUE to specify if the data points should be
# plotted back-to-from relative to the view plane or not. If FALSE, the
# plotting will be faster.
# 2002-03-15
# * Changed the default value of cex, col, pch and type.
# * Added the Rdocs.
# 2002-03-14
# * Added plot3d() and points3d().
# * Created from Ben Bolker's interesting email about persp() today.
############################################################################
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