Re: [Rd] Sweave support added to rgl package

From: Duncan Murdoch <murdoch.duncan_at_gmail.com>
Date: Wed, 20 Apr 2011 20:56:36 -0400

On 20/04/2011 7:10 PM, Dominick Samperi wrote:

> On Wed, Apr 20, 2011 at 2:29 PM, Duncan Murdoch
> <murdoch.duncan_at_gmail.com>  wrote:
>> On 20/04/2011 1:52 PM, Dominick Samperi wrote:

>>>
>>> On Tue, Apr 19, 2011 at 2:18 PM, Duncan Murdoch
>>> <murdoch.duncan_at_gmail.com> wrote:
>>>> I have just committed some code to the rgl package on
>>>> https://r-forge.r-project.org/projects/rgl/ to allow rgl images to be
>>>> inserted into Sweave documents. (This is not in the CRAN version yet.)
>>>> It
>>>> makes use of the custom graphics driver support added by Brian Ripley.
>>>>
>>>> In R-devel (which will become R 2.14.0 next spring in New Zealand, next
>>>> fall
>>>> in most other places), usage is quite straightforward. For
>>>> example, code like this in a Sweave document:
>>>>
>>>> <<fig=true, grdevice=rgl.Sweave, pdf=false, stayopen=TRUE>>=
>>>> x<- rnorm(100); y<- rnorm(100); z<- rnorm(100)
>>>> plot3d(x, y, z)
>>>> @
>>>>
>>>> will insert a .png snapshot of the figure. Because that chunk has
>>>> "stayopen=TRUE", it can be followed by another chunk to add
>>>> to the figure, e.g.
>>>>
>>>> <<fig=true, grdevice=rgl.Sweave, pdf=false>>=
>>>> lines3d(x[1:10], y[1:10], z[1:10], col="red")
>>>> @
>>>>
>>>> All of this is possible in R 2.13.0, but it takes more work: see the
>>>> ?rgl.Sweave help page.
>>>>
>>>> I will eventually add postscript and PDF output options as well, and
>>>> perhaps
>>>> some support for the LaTeX movie15 package, but those are not there
>>>> yet.
>>>> Comments or bug reports are welcome.
>>>>
>>>> Duncan Murdoch
>>>
>>> I inserted your example into testrgl.Rnw under R 2.13.0, with
>>> Sweave.snapshot()
>>> at the end of both chunks, but things did not work as expected.
>>>
>>> I used:
>>> $ R CMD Sweave testrgl.Rnw
>>> $ pdflatex tesetrgl
>>> (view testrgl.pdf)
>>>
>>> When R CMD Sweave is run the graphics is displayed interactively.
>>
>> That's unavoidable as far as I know.  I don't think there's a general
>> purpose way to tell OpenGL to render in the background, so it works by
>> rendering on screen, then copying a bitmap to the .png file.

>>>
>>> There is no graphics in the PDF file, even though both .png files
>>> are read when pdflatex is run.
>>
>> Do they look okay?  One possible problem is that you may have asked for a
>> bitmap too big for your hardware to render, in which case those png files
>> will end up with junk (probably blank).  Setting resolution=100 in the chunk
>> headers will do it more coarsely.  (The default is 300 dpi.)  The same
>> effect comes from width=1, height=1  (or some other small numbers).
>>
>> Duncan Murdoch
>>
>
> The resolution=100 tip fixed the problem, thanks.

I'll see if I am skipping over some error message in there. It would be much better for Sweave to fail with an error than generate empty images.

 > Now I see the snapshots

> in the PDF file. Using this in a package will certainly change the
> user experience,
> but it moves away from the traditional batch-oriented R package
> processing, it seems to me.

I don't follow that.

> The idea of adding support for movies and 3D graphics to Sweave/PDF files > sounds very interesting and revolutionary.

Movies will likely be pretty slow. I think you'll want caching of some sort if you want to produce those.

Duncan Murdoch

>
> Dominick



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