[R] Tutorial on rgl Graphics

[Duncan Murdoch]

On 7/25/2008 12:20 PM, Tom La Bone wrote:
> 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?

Not very easily.  Now you can ask for text of a letter "o" and that is 
not too bad.  You might be able to do it using "sprites".

Duncan Murdoch

> 
> 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
>> 
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>> and provide commented, minimal, self-contained, reproducible code.
>> 
>> 
>