Re: [R] Tutorial on rgl Graphics

From: Tom La Bone <booboo_at_gforcecable.com>
Date: Fri, 25 Jul 2008 08:01:29 -0700 (PDT)

After looking around a bit more I found the example I was looking for -- plotlm3d, which I found on the R wiki

     http://wiki.r-project.org/rwiki/doku.php?id=graph_gallery:new-graphics

The original author was John Fox, and it was modified by Jose Claudio Faria and Duncan Murdoch. Below is a simplified version of the function and two examples. One example was presented as a test of the function and it works fine. The second example is the plot I want to make and I can't seem to get the scale on the x and y axes correct. Being unfamiliar with rgl, can someone provide a hint on how to get the scales right? Thanks for the help.

Tom

plotlm3d <- function (x, y, z,

                      surface        = T,
                      model          = 'z ~ x + y',
                      simple.axes    = T,
                      box            = F,
                      xlab           = deparse(substitute(x)),
                      ylab           = deparse(substitute(y)),
                      zlab           = deparse(substitute(z)),
                      surface.col    = c('blue', 'orange', 'red', 'green',
                                         'magenta', 'cyan', 'yellow',
'gray', 'brown'),
                      point.col      = 'yellow',
                      grid.col       = material3d("color"),
                      grid           = T,
                      grid.lines     = 26,
                      sphere.factor  = 1,
                      threshold      = 0.01)
{
  require(rgl)
  require(mgcv)
  xlab; ylab; zlab
  size <- max(c(x,y,z))/100 * sphere.factor   if (size > threshold)
    spheres3d(x, y, z, color = point.col, radius = size)   else
    points3d(x, y, z, color = point.col)   aspect3d(c(1, 1, 1))
  if (surface) {
    xvals <- seq(min(x), max(x), length = grid.lines)     yvals <- seq(min(y), max(y), length = grid.lines)     dat <- expand.grid(x = xvals, y = yvals)     for (i in 1:length(model)) {
      mod <- lm(formula(model[i]))
      zhat <- matrix(predict(mod, newdata = dat), grid.lines, grid.lines)
      surface3d(xvals, yvals, zhat, color = surface.col[i], alpha = 0.5, lit
= F)
      if (grid)
        surface3d(xvals, yvals, zhat, color = grid.col, alpha = 0.5,
        lit = F, front = 'lines', back = 'lines') }}
  if(simple.axes) {
    axes3d(c('x', 'y', 'z'))
    title3d(xlab = xlab, ylab = ylab, zlab = zlab)   }
  else
    decorate3d(xlab = xlab, ylab = ylab, zlab = zlab, box = box) }

#This is an example of a 3D scatterplot that works fine
x <- c( 274, 180, 375, 205, 86, 265, 98, 330, 195, 53,

       430, 372, 236, 157, 370)
y <- c(2450, 3254, 3802, 2838, 2347, 3782, 3008, 2450, 2137, 2560,

      4020, 4427, 2660, 2088, 2605)
z <- c( 162, 120, 223, 131, 67, 169, 81, 192, 116, 55,

       252, 232, 144, 103, 212)
open3d()
plotlm3d(x, y, z,

         surface = T,
         model   = 'z ~ x + y',
         xlab    = 'x',
         ylab    = 'y',
         zlab    = 'z')

#This is the plot I am trying to make - scales on x and y axes are wrong

x <- c(0.3405,0.1220,0.1028,0.08451,0.05668,0.0345,0.003788,0.002121)
y <- c(0.3460,0.1227,0.1097,0.09666,0.07677,0.06278,0.02168,0.01303)
z <- c(2720,1150,1010,790,482,358,78,35)
open3d()
plotlm3d(x, y, z,
         surface = T,
         model   = 'z ~ x + y - 1',
         xlab    = 'x',
         ylab    = 'y',
         zlab    = 'z')



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