Re: [R] Tutorial on rgl Graphics

From: Duncan Murdoch <murdoch_at_stats.uwo.ca>
Date: Fri, 25 Jul 2008 14:14:17 -0400

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
>>
>> ______________________________________________
>> R-help_at_r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>

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```
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