Re: [R] Tutorial on rgl Graphics

From: Tom La Bone <booboo_at_gforcecable.com>
Date: Fri, 25 Jul 2008 09:20:39 -0700 (PDT)

On further experimentation I find that "points" (via points3d) serve my purpose well (instead of the much prettier but more troublesome spheres). The default "point" appears to be a square. Is there a way to make it a circle?

Tom

Duncan Murdoch-2 wrote:

> 
> On 7/25/2008 11:01 AM, Tom La Bone wrote:

>> 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')
> 
> 
> I think you're seeing the effect of the inaccurate bounding box 
> calculation described in ?spheres3d.  The problem is that you're asking 
> for a sphere, but your axes are on wildly different scales.  The 
> bounding box calculation for that situation fails.
> 
> You can work around this by telling rgl to ignore the extent of the 
> spheres (via par3d(ignoreExtent=TRUE)), and plot some points in the 
> corners of the bounding box you really want.  Set their alpha to 0 and 
> they'll be invisible.
> 
> Some day I'll probably fix this, but it's likely to be a while.
> 
> Duncan Murdoch
> 
> ______________________________________________
> R-help_at_r-project.org mailing list
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 

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