Sweave support added to rgl package
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Sweave support added to rgl package
 
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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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
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This is great news Duncan! If you do consider adding support for movie15, the Asymptote graphics language may be handy: http://asymptote.sourceforge.net/ Asymptote can embed 3D graphs into LaTeX documents that are fully zoomable/manipulatable. It also uses LaTeX to typeset the figure text. -Charlie
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering Humboldt State University |
Re: Sweave support added to rgl package
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In reply to this post by Duncan Murdoch-2
On Tue, Apr 19, 2011 at 2:18 PM, Duncan Murdoch
<[hidden email]> 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. There is no graphics in the PDF file, even though both .png files are read when pdflatex is run. Thanks, Dominick ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Sweave support added to rgl package
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On 20/04/2011 1:52 PM, Dominick Samperi wrote:
> On Tue, Apr 19, 2011 at 2:18 PM, Duncan Murdoch > <[hidden email]> 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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Sweave support added to rgl package
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In reply to this post by Sharpie
On 20/04/2011 1:28 PM, Sharpie wrote:
> Duncan Murdoch-2 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 > > > > This is great news Duncan! > > If you do consider adding support for movie15, the Asymptote graphics > language may be handy: > > http://asymptote.sourceforge.net/ > > Asymptote can embed 3D graphs into LaTeX documents that are fully > zoomable/manipulatable. It also uses LaTeX to typeset the figure text. Thanks. That doesn't look easy, but it would indeed be a nice addition. Duncan Murdoch > -Charlie > > > ----- > Charlie Sharpsteen > Undergraduate-- Environmental Resources Engineering > Humboldt State University > -- > View this message in context: http://r.789695.n4.nabble.com/Sweave-support-added-to-rgl-package-tp3461163p3463653.html > Sent from the R devel mailing list archive at Nabble.com. > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Sweave support added to rgl package
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In reply to this post by Duncan Murdoch-2
On Wed, Apr 20, 2011 at 2:29 PM, Duncan Murdoch
<[hidden email]> wrote: > On 20/04/2011 1:52 PM, Dominick Samperi wrote: >> >> On Tue, Apr 19, 2011 at 2:18 PM, Duncan Murdoch >> <[hidden email]> 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. 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. The idea of adding support for movies and 3D graphics to Sweave/PDF files sounds very interesting and revolutionary. Dominick ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Sweave support added to rgl package
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On 20/04/2011 7:10 PM, Dominick Samperi wrote:
> On Wed, Apr 20, 2011 at 2:29 PM, Duncan Murdoch > <[hidden email]> wrote: >> On 20/04/2011 1:52 PM, Dominick Samperi wrote: >>> >>> On Tue, Apr 19, 2011 at 2:18 PM, Duncan Murdoch >>> <[hidden email]> 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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Sweave support added to rgl package
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I've just committed some changes to rgl that will probably detect
bitmaps that are specified to be too large. As well, Brian Ripley backported some of the R-devel additions to the RweaveLatex driver, so now R 2.13.0-patched (revision 55572 or newer) should work as well as R-devel. Duncan Murdoch On 20/04/2011 8:56 PM, Duncan Murdoch wrote: > On 20/04/2011 7:10 PM, Dominick Samperi wrote: > > On Wed, Apr 20, 2011 at 2:29 PM, Duncan Murdoch > > <[hidden email]> wrote: > >> On 20/04/2011 1:52 PM, Dominick Samperi wrote: > >>> > >>> On Tue, Apr 19, 2011 at 2:18 PM, Duncan Murdoch > >>> <[hidden email]> 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 > ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
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