Handling and plotting plotting lists.

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Description

S3 method plot.plist and function plotdev plot the plotting list to the current device. Changes can be made to the perspective view, to the lighting and shading, or to make colors transparent.

getplist and setplist retrieve and store information in the plotting list.

selectplist selects parts from the plotting list, based on a user-defined function.

Usage

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getplist()
setplist(plist)
plotdev(...)
## S3 method for class 'plist'
 plot(x, ...) 
selectplist(plist, SS)

Arguments

x, plist

The plotting list as generated (invisibly) by any of the 3D plotting functions.

SS

Function which tests points for inclusion in the plotting list. It should take as argument three vectors (x, y, z) and return a vector of equal length that is either TRUE or FALSE, denoting whether the point should be selected or not.

...

Additional arguments to change the view or coloration. Supported arguments to change the view are : theta, phi, xlim, ylim, zlim, d, r, scale, expand. See perspbox, persp.

Supported arguments to change the lighting, or coloration are : ltheta, lphi, shade, lighting. See jet.col.

Details

All 3-D functions from package plot3D produce or update a plotting list that is local to the package. One can access this plotting list via getplist and setplist. The list is used to plot when, in a 3-D function, the argument plot is TRUE or via function plotdev.

When new 3-D objects are added to a plot, using the add argument of the plotting functions, then everything except the axes, is redrawn on top of what was already there. This means that several object will be drawn multiple times, and this may clutter the output. This may not be visible on your screen, but it may become apparent when exported. Use plotdev to create clean figures, where every object is drawn only once.

The plotting list can contain the following items:

  • mat, the viewing transformation matrix, a 4 x 4 matrix suitable for projecting 3D coordinates (x, y, z) into the 2D plane using homogeneous 4D coordinates (x,y,z,v).

    It can be used to superimpose additional graphical elements on the 3D plot, by any function that is defined on persp.

    It can also be used to add lines, arrows or points, using the function trans3D.

  • plt, with original plt parameters and the plt parameters used for the main frame.

  • persp, with settings for the perspective box.

  • xlim, ylim, zlim, with ranges.

  • scalefac, the scaling factors in x, y and z direction, used e.g. for shading.

  • dot other plotting parameters passed to persp.

  • colkey, numkey, with settings for the color key(s).

  • poly, segm, pt, CIpt, labels, arr the information for drawing polygons, segments, points, points with confidence intervals, labels and arrows, that are part of the plot.

For the item poly the elements are:

  • x, y, z : A matrix with typically 4 or 5 rows, the first rows defining the x-, y- or z- values of each polygon, the last row contains NA (and which therefore terminates a polygon).

  • col: a vector with the colors for the facets of each polygon.

  • lwd, lty, border: a vector with the line widths, line type and colors for the border of each polygon. (note in R-function polygon, passing a vector of line widths is not implemented; therefore, only the first value of lwd will be used for all polygons).

    When plot.plist is called, the projection depth is calculated and used to sort the facets and function polygon used to draw them.

Value

Returns the updated plotting list.

Note

Once a 3D plot has been generated, a new device can be opened and plotdev used to plot also on this device.

plotdev and plot(getplist()) are the same.

In an extension package, plot3Drgl, a similar function, plotrgl, plots the graphs to the device opened with rgl. This allows interactive zooming, rotating, etc...

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

Examples

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# save plotting parameters                            
 pm   <- par("mfrow")
 pmar <- par("mar")

## ========================================================================
## The volcano
## ========================================================================

 par(mfrow = c(2, 2), mar = c(2, 2, 2, 2))

# The volcano at lower resolution
 x <- seq(1, nrow(volcano), by = 2)
 y <- seq(1, ncol(volcano), by = 2)
 V <- volcano[x,y]

 persp3D(z = V)

# rotate
 plotdev(theta = 0)

# light and transparence
 plotdev(lighting  = TRUE, lphi = 90, alpha = 0.6)  

# zoom
 plotdev(xlim = c(0.2, 0.6), ylim = c(0.2, 0.6), phi = 60) 
 
## ========================================================================
## Two spheres 
## ========================================================================

 par(mfrow = c(1, 1), mar = c(0, 0, 0, 0))

# create a sphere
 M  <- mesh(seq(0, 2*pi, length.out = 30),
            seq(0,   pi, length.out = 30))
 u  <- M$x ; v  <- M$y

 x <- cos(u)*sin(v)
 y <- sin(u)*sin(v)
 z <- cos(v)

 surf3D(x = 2*x, y = 2*y, z = 2*z, 
        colvar = NULL, lighting = TRUE, #plot = FALSE,
        facets = NA, col = "blue", lwd = 5)
 
 surf3D(x, y, z, colvar = NULL, lighting = TRUE, 
        col = "red", add = TRUE)

 names(getplist())

# plot with different view:
 plotdev(phi = 0)  
## Not run:   # will plot same 3-D graph to pdf
 pdf(file = "save.pdf")
 plotdev()
 dev.off()

## End(Not run)
             
## ========================================================================
## Two spheres and two planes 
## ========================================================================

 par(mar = c(2, 2, 2, 2))

# equation of a sphere
 M  <- mesh(seq(0, 2*pi, length.out = 100),                                     -
            seq(0,   pi, length.out = 100))
 u  <- M$x ; v  <- M$y

 x <- cos(u)*sin(v)
 y <- sin(u)*sin(v)
 z <- cos(v)

 surf3D(x, y, z, colvar = z, 
        theta = 45, phi = 20, bty = "b",
        xlim = c(-1.5, 1.5), ylim = c(-1, 2), 
        zlim = c(-1.5, 1.5), plot = FALSE)

# add a second sphere, shifted 1 unit to the right on y-axis; 
# no facets drawn for this sphere 
 surf3D (x, y+1, z, colvar = z, add = TRUE, 
         facets = FALSE, plot = FALSE)

# define a plane at z = 0
 Nx <- 100
 Ny <- 100
  
 x <- seq(-1.5, 1.5, length.out = Nx)
 y <- seq(-1, 2, length.out = Ny)

 image3D (x = x, y = y, z = 0, add = TRUE, colvar = NULL, 
          col = "blue", facets = TRUE, plot = FALSE)

# another, small plane at y = 0 - here x and y have to be matrices!
 x <- seq(-1., 1., length.out = 50)
 z <- seq(-1., 1., length.out = 50)
 
 image3D (x = x, y = 0, z = z, colvar = NULL, 
         add = TRUE, col = NA, border = "blue", 
         facets = TRUE, plot = TRUE)       

## Not run:   # rotate 
 for (angle in seq(0, 360, by = 10)) 
   plotdev(theta = angle)

## End(Not run)

## ========================================================================
## Zooming, rescaling, lighting,...
## ========================================================================

 par(mfrow = c(2, 2)) 

# The volcano
 x <- seq(1, nrow(volcano), by = 2)
 y <- seq(1, ncol(volcano), by = 2)
 V <- volcano[x,y]
# plot the volcano
 persp3D (x, y, z = V, colvar = V, theta = 10, phi = 20, 
          box = FALSE, scale = FALSE, expand = 0.3, 
          clim = range(V), plot = FALSE)

# add a plane (image) at z = 170; jetcolored, transparant: only border
 image3D(x, y, z = 170, add = TRUE, clim = range(V), 
         colvar = V, facets = NA, plot = FALSE, colkey = FALSE)

# add a contour (image) at z = 170; jetcolored, 
 contour3D(x, y, z = 170, add = TRUE, clim = range(V),
           colvar = V, plot = FALSE, colkey = FALSE)

# plot it  - 
 plot(getplist())   #  same as plotdev()

# plot but with different expansion
 plotdev(expand = 1)

# other perspective, and shading
 plotdev(d = 2, r = 10, shade = 0.3)
    
# zoom and rotate
 plotdev(xlim = c(10, 30), ylim = c(20, 30), phi = 50)

## ========================================================================
## Using setplist
## ========================================================================

 polygon3D(runif(3), runif(3), runif(3))
# retrieve plotting list
 plist <- getplist()
 names(plist)
 plist$poly
# change copy of plotting list
 plist$poly$col <- "red"
# update internal plotting list
 setplist(plist)
# plot updated list
 plotdev()
 

## ========================================================================
## Using selectplist
## ========================================================================

 polygon3D(runif(10), runif(10), runif(10), col = "red", 
   alpha = 0.2, plot = FALSE, ticktype = "detailed", 
   xlim = c(0,1), ylim = c(0, 1), zlim = c(0, 1))
 polygon3D(runif(10)*0.5, runif(10), runif(10), col = "yellow", 
   alpha = 0.2, plot = FALSE, add = TRUE)
 polygon3D(runif(10)*0.5+0.5, runif(10), runif(10), col = "green", 
   alpha = 0.2, plot = FALSE, add = TRUE)
 points3D(runif(10), runif(10), runif(10), col = "blue", 
   add = TRUE, plot = FALSE)
 segments3D(x0 = runif(10), y0 = runif(10), z0 = runif(10), 
   x1 = runif(10), y1 = runif(10), z1 = runif(10), 
   colvar = 1:10, add = TRUE, lwd = 3)

# retrieve plotting list
 plist <- getplist()

# selection function 
 SS <- function (x, y, z)  {
   sel <- rep(TRUE, length.out = length(x))
   sel[x < 0.5] <- FALSE
   return(sel)
 } 
# The whole polygon will be removed or kept.  
 plot(x = selectplist(plist, SS), 
   xlim = c(0, 1), ylim = c(0, 1), zlim = c(0, 1))

# restore plotting parameters
 par(mfrow = pm)
 par(mar = pmar)