scatter3d

From car v2.0-0 by John Fox

Three-Dimensional Scatterplots and Point Identification

The scatter3d function uses the rgl package to draw 3D scatterplots with various regression surfaces. The function identify3d allows you to label points interactively with the mouse: Press the right mouse button (on a two-button mouse) or the centre button (on a three-button mouse), drag a rectangle around the points to be identified, and release the button. Repeat this procedure for each point or set of nearby points to be identified. To exit from point-identification mode, click the right (or centre) button in an empty region of the plot.

Keywords: hplot

Usage

scatter3d(x, ...)

## S3 method for class 'formula':
scatter3d(formula, data, subset, xlab, ylab, zlab, labels, ...)

## S3 method for class 'default':
scatter3d(x, y, z,
	  xlab=deparse(substitute(x)), ylab=deparse(substitute(y)),
	  zlab=deparse(substitute(z)), axis.scales=TRUE, revolutions=0, 
      bg.col=c("white", "black"),
	  axis.col=if (bg.col == "white") c("darkmagenta", "black", "darkcyan")
		  else c("darkmagenta", "white", "darkcyan"),
	  surface.col=c("blue", "green", "orange", "magenta", "cyan", "red", 
      "yellow", "gray"),
	  neg.res.col="red", pos.res.col="green",
	  square.col=if (bg.col == "white") "black" else "gray", point.col="yellow",
	  text.col=axis.col, grid.col=if (bg.col == "white") "black" else "gray",
	  fogtype=c("exp2", "linear", "exp", "none"),
	  residuals=(length(fit) == 1), surface=TRUE, fill=TRUE, grid=TRUE, 
      grid.lines=26, df.smooth=NULL, df.additive=NULL,
	  sphere.size=1, threshold=0.01, speed=1, fov=60, 
	  fit="linear", groups=NULL, parallel=TRUE, ellipsoid=FALSE, level=0.5,
	  id.method=c("mahal", "xz", "y", "xyz", "identify", "none"), 
	  id.n=if (id.method == "identify") Inf else 0,
	  labels=as.character(seq(along=x)), offset = ((100/length(x))^(1/3)) * 0.02,
	  model.summary=FALSE, ...)
    
identify3d(x, y, z, axis.scales=TRUE, groups = NULL, labels = 1:length(x),
	col = c("blue", "green", "orange", "magenta", "cyan", "red", "yellow", "gray"),
	offset = ((100/length(x))^(1/3)) * 0.02)

Arguments

formula: ``model'' formula, of the form y ~ x + z or (to plot by groups) y ~ x + z | g, where g evaluates to a factor or other variable dividing the data into groups.
data: data frame within which to evaluate the formula.
subset: expression defining a subset of observations.
x: variable for horizontal axis.
y: variable for vertical axis (response).
z: variable for out-of-screen axis.
xlab, ylab, zlab: axis labels.
axis.scales: if TRUE, label the values of the ends of the axes. Note: For identify3d to work properly, the value of this argument must be the same as in scatter3d.
revolutions: number of full revolutions of the display.
bg.col: background colour; one of "white", "black".
axis.col: colours for axes; if axis.scales is FALSE, then the second colour is used for all three axes.
surface.col: vector of colours for regression planes, used in the order specified by fit.
neg.res.col, pos.res.col: colours for lines representing negative and positive residuals.
square.col: colour to use to plot squared residuals.
point.col: colour of points.
text.col: colour of axis labels.
grid.col: colour of grid lines on the regression surface(s).
fogtype: type of fog effect; one of "exp2", "linear", "exp", "none".
residuals: plot residuals if TRUE; if residuals="squares", then the squared residuals are shown as squares (using code adapted from Richard Heiberger). Residuals are available only when there is one surface plotted.
surface: plot surface(s) (TRUE or FALSE).
fill: fill the plotted surface(s) with colour (TRUE or FALSE).
grid: plot grid lines on the regression surface(s) (TRUE or FALSE).
grid.lines: number of lines (default, 26) forming the grid, in each of the x and z directions.
df.smooth: degrees of freedom for the two-dimensional smooth regression surface; if NULL (the default), the gam function will select the degrees of freedom for a smoothing spline by generalized
df.additive: degrees of freedom for each explanatory variable in an additive regression; if NULL (the default), the gam function will select degrees of freedom for the smoothing splines by generalized cross-validation; if a positiv
sphere.size: relative sizes of spheres representing points; the actual size is dependent on the number of observations.
threshold: if the actual size of the spheres is less than the threshold, points are plotted instead.
speed: relative speed of revolution of the plot.
fov: field of view (in degrees); controls degree of perspective.
fit: one or more of "linear", "quadratic", "smooth", "additive"; to display fitted surface(s); partial matching is supported -- e.g., c("lin", "quad").
groups: if NULL (the default), no groups are defined; if a factor, a different surface or set of surfaces is plotted for each level of the factor; in this event, the colours in plane.col are used successively for the points, s
parallel: when plotting surfaces by groups, should the surfaces be constrained to be parallel? A logical value, with default TRUE.
ellipsoid: plot concentration ellipsoid(s) (TRUE or FALSE).
level: expected proportion of bivariate-normal observations included in the concentration ellipsoid(s); default is 0.5.
id.method: if "mahal" (the default), relatively extreme points are identified automatically according to their Mahalanobis distances from the centroid (point of means); if "identify", points are identified interactively by right-cli
id.n: Number of relatively extreme points to identify automatically (default, 0 unless id.method="identify").
model.summary: print summary or summaries of the model(s) fit (TRUE or FALSE). scatter3d rescales the three variables internally to fit in the unit cube; this rescaling will affect regression coefficients.
labels: text labels for the points, one for each point; in the default method defaults to the observation indices, in the formula method to the row names of the data.
col: colours for the point labels, given by group. There must be at least as many colours as groups; if there are no groups, the first colour is used. Normally, the colours would correspond to the plane.col argument to scatter3d
offset: vertical displacement for point labels (to avoid overplotting the points).
...: arguments to be passed down.

Value

scatter3d does not return a useful value; it is used for its side-effect of creating a 3D scatterplot. identify3d returns the labels of the identified points.

Note

You have to install the rgl package to produce 3D plots.

References

Fox, J. and Weisberg, S. (2011) An R Companion to Applied Regression, Second Edition, Sage.

Examples

if(interactive() && require(rgl) && require(mgcv)){
scatter3d(prestige ~ income + education, data=Duncan)
Sys.sleep(5) # wait 5 seconds
scatter3d(prestige ~ income + education | type, data=Duncan)
Sys.sleep(5)
scatter3d(prestige ~ income + education | type, surface=FALSE, 
	ellipsoid=TRUE, revolutions=3, data=Duncan)
scatter3d(prestige ~ income + education, fit=c("linear", "additive"),
	data=Prestige)
	}
	# drag right mouse button to identify points, click right button in open area to exit
scatter3d(prestige ~ income + education, data=Duncan, id.method="identify")
scatter3d(prestige ~ income + education | type, data=Duncan, id.method="identify")

Documentation reproduced from package car, version 2.0-0, License: GPL (>= 2)

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