Default Panel Function for cloud

Default panel functions controlling cloud and wireframe displays.

Usage

panel.cloud(x, y, subscripts, z,
            groups = NULL,
            perspective = TRUE,
            distance = if (perspective) 0.2 else 0, 
            xlim, ylim, zlim,
            panel.3d.cloud = "panel.3dscatter",
            panel.3d.wireframe = "panel.3dwire",
            screen = list(z = 40, x = -60),
            R.mat = diag(4), aspect = c(1, 1),
            par.box = NULL,
            xlab, ylab, zlab,
            xlab.default, ylab.default, zlab.default,
            scales.3d,
            proportion = 0.6,
            wireframe = FALSE,
            scpos,
            ...,
            at,
            identifier = "cloud")
panel.wireframe(...)
panel.3dscatter(x, y, z, rot.mat, distance,
                groups, type = "p",
                xlim, ylim, zlim,
                xlim.scaled, ylim.scaled, zlim.scaled,
                zero.scaled,
                col, col.point, col.line,
                lty, lwd, cex, pch, fill,
                cross, ..., .scale = FALSE, subscripts,
                identifier = "3dscatter")
panel.3dwire(x, y, z, rot.mat = diag(4), distance,
             shade = FALSE,
             shade.colors.palette = trellis.par.get("shade.colors")$palette,
             light.source = c(0, 0, 1000),
             xlim, ylim, zlim, 
             xlim.scaled,
             ylim.scaled,
             zlim.scaled,
             col = if (shade) "transparent" else "black",
             lty = 1, lwd = 1,
             alpha,
             col.groups = superpose.polygon$col,
             polynum = 100,
             ...,
             .scale = FALSE,
             drape = FALSE,
             at,
             col.regions = regions$col,
             alpha.regions = regions$alpha,
             identifier = "3dwire")
makeShadePalette(col.regions, ..., min = 0.05, pref = 0.75)

Arguments

x, y, z

numeric (or possibly factors) vectors representing the data to be displayed. The interpretation depends on the context. For panel.cloud these are essentially the same as the data passed to the high level plot (except if formula was a matrix, the appropriate x and y vectors are generated). By the time they are passed to panel.3dscatter and panel.3dwire, they have been appropriately subsetted (using subscripts) and scaled (to lie inside a bounding box, usually the [-0.5, 0.5] cube).

Further, for panel.3dwire, x and y are shorter than z and represent the sorted locations defining a rectangular grid. Also in this case, z may be a matrix if the display is grouped, with each column representing one surface.

In panel.cloud (called from wireframe) and panel.3dwire, x, y and z could also be matrices (of the same dimension) when they represent a 3-D surface parametrized on a 2-D grid.

subscripts

index specifying which points to draw. The same x, y and z values (representing the whole data) are passed to panel.cloud for each panel. subscripts specifies the subset of rows to be used for the particular panel.

groups

specification of a grouping variable, passed down from the high level functions.

perspective

logical, whether to plot a perspective view. Setting this to FALSE is equivalent to setting distance to 0

distance

numeric, between 0 and 1, controls amount of perspective. The distance of the viewing point from the origin (in the transformed coordinate system) is 1 / distance. This is described in a little more detail in the documentation for cloud

screen

A list determining the sequence of rotations to be applied to the data before being plotted. The initial position starts with the viewing point along the positive z-axis, and the x and y axes in the usual position. Each component of the list should be named one of "x", "y" or "z" (repetitions are allowed), with their values indicating the amount of rotation about that axis in degrees.

R.mat

initial rotation matrix in homogeneous coordinates, to be applied to the data before screen rotates the view further.

par.box

graphical parameters for box, namely, col, lty and lwd. By default obtained from the parameter box.3d.

xlim, ylim, zlim

limits for the respective axes. As with other lattice functions, these could each be a numeric 2-vector or a character vector indicating levels of a factor.

panel.3d.cloud, panel.3d.wireframe

functions that draw the data-driven part of the plot (as opposed to the bounding box and scales) in cloud and wireframe. This function is called after the ‘back’ of the bounding box is drawn, but before the ‘front’ is drawn.

Any user-defined custom display would probably want to change these functions. The intention is to pass as much information to this function as might be useful (not all of which are used by the defaults). In particular, these functions can expect arguments called xlim, ylim, zlim which give the bounding box ranges in the original data scale and xlim.scaled, ylim.scaled, zlim.scaled which give the bounding box ranges in the transformed scale. More arguments can be considered on request.

aspect

aspect as in cloud

xlab, ylab, zlab

Labels, have to be lists. Typically the user will not manipulate these, but instead control this via arguments to cloud directly.

xlab.default

for internal use

ylab.default

for internal use

zlab.default

for internal use

scales.3d

list defining the scales

proportion

numeric scalar, gives the length of arrows as a proportion of the sides

scpos

A list with three components x, y and z (each a scalar integer), describing which of the 12 sides of the cube the scales should be drawn. The defaults should be OK. Valid values are x: 1, 3, 9, 11; y: 8, 5, 7, 6 and z: 4, 2, 10, 12. (See comments in the source code of panel.cloud to see the details of this enumeration.)

wireframe

logical, indicating whether this is a wireframe plot

drape

logical, whether the facets will be colored by height, in a manner similar to levelplot. This is ignored if shade=TRUE.

at

When drape = TRUE in wireframe, the facets defining the surface are colored as a function of (average) height, similar to levelplot. at is a numeric vector giving the breakpoints along the z-axis where colors change.

col.regions

vector of colors to be used in conjunction with at when drape = TRUE.

In makeShadePalette, which can be used to define a shading palette (see below), col.regions is an initial vector defining the base color (as a function of height) that is then adjusted according to irradiance and reflectance.

alpha.regions

numeric scalar controlling transparency when drape = TRUE.

rot.mat

4x4 transformation matrix in homogeneous coordinates. This gives the rotation matrix combining the screen and R.mat arguments to panel.cloud

type

Character vector, specifying type of cloud plot. Can include one or more of "p", "l", "h" or "b". "p" and "l" mean ‘points’ and ‘lines’ respectively, and "b" means ‘both’. "h" stands for ‘histogram’, and causes a line to be drawn from each point to the X-Y plane (i.e., the plane representing z = 0), or the lower (or upper) bounding box face, whichever is closer.

xlim.scaled, ylim.scaled, zlim.scaled

axis limits (after being scaled to the bounding box)

zero.scaled

z-axis location (after being scaled to the bounding box) of the X-Y plane in the original data scale, to which lines will be dropped (if within range) from each point when type = "h"

cross

logical, defaults to TRUE if pch = "+". panel.3dscatter can represent each point by a 3d ‘cross’ of sorts (it's much easier to understand looking at an example than from a description). This is different from the usual pch argument, and reflects the depth of the points and the orientation of the axes. This argument indicates whether this feature will be used.

This is useful for two reasons. It can be set to FALSE to use "+" as the plotting character in the regular sense. It can also be used to force this feature in grouped displays.

shade

logical, indicating whether the surface is to be colored using an illumination model with a single light source

shade.colors.palette

a function (or the name of one) that is supposed to calculate the color of a facet when shading is being used. Three pieces of information are available to the function: first, the cosine of the angle between the incident light ray and the normal to the surface (representing foreshortening); second, the cosine of half the angle between the reflected ray and the viewing direction (useful for non-Lambertian surfaces); and third, the scaled (average) height of that particular facet with respect to the total plot z-axis limits.

All three numbers should be between 0 and 1. The shade.colors.palette function should return a valid color. The default function is obtained from the trellis settings using makeShadePalette.

min

numeric, between 0 and 1, giving a minimum saturation in makeShadePalette

pref

numeric, giving a power that is applied to reflectance value before it is used to ‘darken’ the colors.

light.source

a 3-vector representing (in cartesian coordinates) the light source. This is relative to the viewing point being (0, 0, 1/distance) (along the positive z-axis), keeping in mind that all observations are bounded within the [-0.5, 0.5] cube

polynum

quadrilateral faces are drawn in batches of polynum at a time. Drawing too few at a time increases the total number of calls to the underlying grid.polygon function, which affects speed. Trying to draw too many at once may be unnecessarily memory intensive. This argument controls the trade-off.

col.groups

colors for different groups

col, col.point, col.line, lty, lwd, cex, pch, fill, alpha

Graphical parameters. Some other arguments (such as lex for line width) may also be passed through the ... argument.

...

other parameters, passed down when appropriate

.scale

Logical flag, indicating whether x, y, and z should be assumed to be in the original data scale and hence scaled before being plotted. x, y, and z are usually already scaled. However, setting .scale=TRUE may be helpful for calls to panel.3dscatter and panel.3dwire in user-supplied panel functions.

identifier

A character string that is prepended to the names of grobs that are created by this panel function.

Details

These functions together are responsible for the content drawn inside each panel in cloud and wireframe. panel.wireframe is a wrapper to panel.cloud, which does the actual work.

panel.cloud is responsible for drawing the content that does not depend on the data, namely, the bounding box, the arrows/scales, etc. At some point, depending on whether wireframe is TRUE, it calls either panel.3d.wireframe or panel.3d.cloud, which draws the data-driven part of the plot.

The arguments accepted by these two functions are different, since they have essentially different purposes. For cloud, the data is unstructured, and x, y and z are all passed to the panel.3d.cloud function. For wireframe, on the other hand, x and y are increasing vectors with unique values, defining a rectangular grid. z must be a matrix with length(x) * length(y) rows, and as many columns as the number of groups.

panel.3dscatter is the default panel.3d.cloud function. It has a type argument similar to panel.xyplot, and supports grouped displays. It tries to honour depth ordering, i.e., points and lines closer to the camera are drawn later, overplotting more distant ones. (Of course there is no absolute ordering for line segments, so an ad hoc ordering is used. There is no hidden point removal.)

panel.3dwire is the default panel.3d.wireframe function. It calculates polygons corresponding to the facets one by one, but waits till it has collected information about polynum facets, and draws them all at once. This avoids the overhead of drawing grid.polygon repeatedly, speeding up the rendering considerably. If shade = TRUE, these attempt to color the surface as being illuminated from a light source at light.source. palette.shade is a simple function that provides the deafult shading colors

Multiple surfaces are drawn if groups is non-null in the call to wireframe, however, the algorithm is not sophisticated enough to render intersecting surfaces correctly.

Author

Deepayan Sarkar Deepayan.Sarkar@R-project.org

See also

cloud, utilities.3d

Examples

wireframe(volcano, shade = TRUE,
          shade.colors.palette = makeShadePalette(hcl.colors(10, "Inferno"),
                                                  pref = 0.2))

wireframe(volcano, shade = TRUE,
          shade.colors.palette = makeShadePalette(hcl.colors(10, "Dark Mint"),
                                                  pref = 0.2))

wireframe(volcano, shade = TRUE,
          shade.colors.palette = makeShadePalette(hcl.colors(10, "Harmonic"),
                                                  pref = 0.2))