R: Default Panel Function for cloud

F_1_panel.cloud {lattice}

R Documentation

Default Panel Function for cloud

Description

These are 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,
                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")

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, col.regions, alpha.regions`	deals with specification of colors when `drape = TRUE` in `wireframe`. `at` can be a numeric vector, `col.regions` a vector of colors, and `alpha.regions` a numeric scalar controlling transparency. The resulting behaviour is similar to `levelplot`, `at` giving the breakpoints along the z-axis where colors change, and the other two determining the colors of the facets that fall in between.
`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.
`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, 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(s)