scatterplot3d {scatterplot3d}

3D Scatter Plot

Description

Plots a three dimensional (3D) point cloud.

Usage

scatterplot3d(x, y=NULL, z=NULL, color=par("col"), pch=par("pch"),
    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, y.axis.offset=1, 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="", asp=NA, ...)

Arguments

x

the coordinates of points in the plot.

y

the y coordinates of points in the plot, optional if x is an appropriate structure.

z

the z coordinates of points in the plot, optional if x is an appropriate structure.

color

colors of points in the plot, optional if x is an appropriate structure. Will be ignored if highlight.3d = TRUE.

pch

plotting "character", i.e. symbol to use.

main

an overall title for the plot.

sub

sub-title.

xlim, ylim, zlim

the x, y and z limits (min, max) of the plot. Note that setting enlarged limits may not work as exactly as expected (a known but unfixed bug).

xlab, ylab, zlab

titles for the x, y and z axis.

scale.y

scale of y axis related to x- and z axis.

angle

angle between x and y axis (Attention: result depends on scaling).

axis

a logical value indicating whether axes should be drawn on the plot.

tick.marks

a logical value indicating whether tick marks should be drawn on the plot (only if axis = TRUE).

label.tick.marks

a logical value indicating whether tick marks should be labeled on the plot (only if axis = TRUE and tick.marks = TRUE).

x.ticklabs, y.ticklabs, z.ticklabs

vector of tick mark labels.

y.margin.add

add additional space between tick mark labels and axis label of the y axis

y.axis.offset

a numeric (default 1) specifying the offset of y axis tick mark labels from the axis, see offset argument of text.

grid

a logical value indicating whether a grid should be drawn on the plot.

box

a logical value indicating whether a box should be drawn around the plot.

lab

a numerical vector of the form c(x, y, len). The values of x and y give the (approximate) number of tickmarks on the x and y axes.

lab.z

the same as lab, but for z axis.

type

character indicating the type of plot: "p" for points, "l" for lines, "h" for vertical lines to x-y-plane, etc.

highlight.3d

points will be drawn in different colors related to y coordinates (only if type = "p" or type = "h", else color will be used).
On some devices not all colors can be displayed. In this case try the postscript device or use highlight.3d = FALSE.

mar

A numerical vector of the form c(bottom, left, top, right) which gives the lines of margin to be specified on the four sides of the plot. See section Values on how to change the setting back to the default / previous setting.

bg

background (fill) color for the open plot symbols given by pch = 21:25.

col.axis, col.grid, col.lab

the color to be used for axis / grid / axis labels.

cex.symbols

the magnification to be used for point symbols.

cex.axis, cex.lab

the magnification to be used for axis annotation and labels relative to the current.

font.axis, font.lab

the font to be used for axis annotation / labels.

lty.axis, lty.grid

the line type to be used for axis / grid.

lty.hide

line style used to plot ‘non-visible’ edges (defaults of the lty.axis style)

lty.hplot

the line type to be used for vertical segments with type = "h".

log

Not yet implemented! A character string which contains "x" (if the x axis is to be logarithmic), "y", "z", "xy", "xz", "yz", "xyz".

asp

numeric, giving the aspect ratio z/x or z/y, see ‘Note’.

...

more graphical parameters can be given as arguments, pch = 16 or pch = 20 may be nice.

Value

xyz.convert

function which converts coordinates from 3D (x, y, z) to 2D-projection (x, y) of scatterplot3d. Useful to plot objects into existing plot.

points3d

function which draws points or lines into the existing plot.

plane3d

function which draws a plane into the existing plot: plane3d(Intercept, x.coef = NULL, y.coef = NULL, lty = "dashed", lty.box = NULL, draw_lines = TRUE, draw_polygon = FALSE, polygon_args = list(border = NA, col = rgb(0,0,0,0.2)), ...). Instead of Intercept a vector containing 3 elements or an (g)lm object can be specified. The argument lty.box allows to set a different line style for the intersecting lines in the box's walls. The arguments draw_lines and draw_polygon allow for choosing whether to represent the plane via line segments or as a solid surface, respectively. The list in polygon_args collects arguments to be passed to the underlying polygon call that draws a solid (or transparent) plane if draw_polygon=TRUE.

box3d

function which “refreshes” the box surrounding the plot.

contour3d

function which draws countour lines into the existing plot: contour3d(f, x.count = 10, y.count = 10, type = "l", lty = "24", x.resolution = 50, y.resolution = 50, ...). The first argument can be an lm object of two dimensions or a function of two arguments. In both cases the dimensions have to be given in the order x, y of the scatterplot3d call. The arguments x.count and y.count specify how many segments should be drawn for each dimension. The arguments x.resolution and y.resolution control the number of locations where the segments have to be evaluated.

par.mar

As the function modifies the par("mar") settings of the current device and needs to keep these in case you add elements to the plot later on, you can change these back via par(object$par.mar) in case you want to add more plots with default margins to the current device.

Note

Some graphical parameters should only be set as arguments in scatterplot3d but not in a previous par() call. One of these is mar, which is also non-standard in another way: Users who want to extend an existing scatterplot3d graphic with another function than points3d, plane3d or box3d, should consider to set par(mar = c(b, l, t, r)) to the value of mar used in scatterplot3d, which defaults to c(5, 3, 4, 3) + 0.1.

Other par arguments may be split into several arguments in scatterplot3d, e.g., for specifying the line type. And finally some of par arguments do not apply here, e.g., many of those for axis calculation. So we recommend to try the specification of graphical parameters at first as arguments in scatterplot3d and only if needed as arguments in previous par() call.

If asp is a finite positive value then the window is set up so that one data unit in the x or y direction (the one that ist plotted horizontally - depends on angle -) is equal in length to asp \times one data unit in the z direction. The variation of asp is only reasonable if the default values x.ticklabs=NULL, y.ticklabs=NULL, z.ticklabs=NULL are not changed.

Author(s)

Uwe Ligges [e-mail], Martin Maechler, Sarah Schnackenberg

References

Ligges, U., and Maechler, M. (2003): Scatterplot3d – an R Package for Visualizing Multivariate Data. Journal of Statistical Software 8(11), 1–20. doi:10.18637/jss.v008.i11

See Also

persp, plot, par.

Examples

  ## On some devices not all colors can be displayed.
  ## Try the postscript device or use highlight.3d = FALSE.

  ## example 1
  z <- seq(-10, 10, 0.01)
  x <- cos(z)
  y <- sin(z)
  scatterplot3d(x, y, z, highlight.3d=TRUE, col.axis="blue",
      col.grid="lightblue", main="scatterplot3d - 1", pch=20, mar=c(0,0,0,0))

  ## example 2
  temp <- seq(-pi, 0, length = 50)
  x <- c(rep(1, 50) %*% t(cos(temp)))
  y <- c(cos(temp) %*% t(sin(temp)))
  z <- c(sin(temp) %*% t(sin(temp)))
  scatterplot3d(x, y, z, highlight.3d=TRUE,
      col.axis="blue", col.grid="lightblue",
      main="scatterplot3d - 2", pch=20)

  ## example 3
  temp <- seq(-pi, 0, length = 50)
  x <- c(rep(1, 50) %*% t(cos(temp)))
  y <- c(cos(temp) %*% t(sin(temp)))
  z <- 10 * c(sin(temp) %*% t(sin(temp)))
  color <- rep("green", length(x))
  temp <- seq(-10, 10, 0.01)
  x <- c(x, cos(temp))
  y <- c(y, sin(temp))
  z <- c(z, temp)
  color <- c(color, rep("red", length(temp)))
  scatterplot3d(x, y, z, color, pch=20, zlim=c(-2, 10),
      main="scatterplot3d - 3")

  ## example 4
  my.mat <- matrix(runif(25), nrow=5)
  dimnames(my.mat) <- list(LETTERS[1:5], letters[11:15])
  my.mat # the matrix we want to plot ...

  s3d.dat <- data.frame(cols=as.vector(col(my.mat)),
      rows=as.vector(row(my.mat)),
      value=as.vector(my.mat))
  scatterplot3d(s3d.dat, type="h", lwd=5, pch=" ",
      x.ticklabs=colnames(my.mat), y.ticklabs=rownames(my.mat),
      color=grey(25:1/40), main="scatterplot3d - 4")

  ## example 5
  data(trees)
  s3d <- scatterplot3d(trees, type="h", highlight.3d=TRUE,
      angle=55, scale.y=0.7, pch=16, main="scatterplot3d - 5")
  # Now adding some points to the "scatterplot3d"
  s3d$points3d(seq(10,20,2), seq(85,60,-5), seq(60,10,-10),
      col="blue", type="h", pch=16)
  # Now adding a regression plane to the "scatterplot3d"
  attach(trees)
  my.lm <- lm(Volume ~ Girth + Height)
  s3d$plane3d(my.lm, lty.box = "solid")
  
  ## example 6; by Martin Maechler
  cubedraw <- function(res3d, min = 0, max = 255, cex = 2, text. = FALSE)
  {
    ## Purpose: Draw nice cube with corners
    cube01 <- rbind(c(0,0,1), 0, c(1,0,0), c(1,1,0), 1, c(0,1,1), # < 6 outer
                    c(1,0,1), c(0,1,0)) # <- "inner": fore- & back-ground
    cub <- min + (max-min)* cube01
    ## visibile corners + lines:
    res3d$points3d(cub[c(1:6,1,7,3,7,5) ,], cex = cex, type = 'b', lty = 1)
    ## hidden corner + lines
    res3d$points3d(cub[c(2,8,4,8,6),     ], cex = cex, type = 'b', lty = 3)
    if(text.)## debug
        text(res3d$xyz.convert(cub), labels=1:nrow(cub), col='tomato', cex=2)
  }
  ## 6 a) The named colors in R, i.e. colors()
  cc <- colors()
  crgb <- t(col2rgb(cc))
  par(xpd = TRUE)
  rr <- scatterplot3d(crgb, color = cc, box = FALSE, angle = 24,
      xlim = c(-50, 300), ylim = c(-50, 300), zlim = c(-50, 300))
  cubedraw(rr)
  ## 6 b) The rainbow colors from rainbow(201)
  rbc <- rainbow(201)
  Rrb <- t(col2rgb(rbc))
  rR <- scatterplot3d(Rrb, color = rbc, box = FALSE, angle = 24,
      xlim = c(-50, 300), ylim = c(-50, 300), zlim = c(-50, 300))
  cubedraw(rR)
  rR$points3d(Rrb, col = rbc, pch = 16)