Re: [R] Sweave: infelicities with lattice graphics
Just a follow-up on this thread, now with R 2.11.1. I was happy back then to use Deepayan's solution for this, under earlier R versions; but it now gives an error and the Sweave-generated .tex file no longer compiles. ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= plot(trellis.last.object()) @ Now, I get the following from Sweave: Error: chunk 46 (label=ortho-xyplot1) Error in !lattice.getStatus(current.plot.saved, prefix = prefix) : invalid argument type Did something in lattice change so that plot(trellis.last.object()) no longer works or needs to be specified differently? -Michael On 7/16/2010 1:14 AM, Deepayan Sarkar wrote: On Thu, Jul 15, 2010 at 1:51 PM, Michael Friendlyfrien...@yorku.ca wrote: In a paper I'm writing using Sweave, I make use of lattice graphics, but don't want to explicitly show (or explain) in the article text the print() wrapper I need in code chunks for the graphs to appear. I can solve this by including each chunk twice, with different options, as in ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= library(nlme) library(lattice) print(xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data)) @ but then, if I decide to change the plotting code, I have to make changes in two places. Is there some feature of Sweave or lattice I've missed that would simplify this? Re-use of code chunks doesn't seem to apply here. I usually use this variant of Duncan's suggestion: ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= plot(trellis.last.object()) @ -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave: infelicities with lattice graphics
On 12/09/2010 11:41 AM, Michael Friendly wrote: Just a follow-up on this thread, now with R 2.11.1. I was happy back then to use Deepayan's solution for this, under earlier R versions; but it now gives an error and the Sweave-generated .tex file no longer compiles. ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= plot(trellis.last.object()) @ Now, I get the following from Sweave: Error: chunk 46 (label=ortho-xyplot1) Error in !lattice.getStatus(current.plot.saved, prefix = prefix) : invalid argument type Did something in lattice change so that plot(trellis.last.object()) no longer works or needs to be specified differently? I don't know if something in lattice has changed, but that doesn't look as though it should work: the code to do the plot was never evaluated. I think you would need eval=TRUE in the first chunk, or ortho-xyplot1-code ahead of the plot command in the second. Duncan Murdoch -Michael On 7/16/2010 1:14 AM, Deepayan Sarkar wrote: On Thu, Jul 15, 2010 at 1:51 PM, Michael Friendlyfrien...@yorku.ca wrote: In a paper I'm writing using Sweave, I make use of lattice graphics, but don't want to explicitly show (or explain) in the article text the print() wrapper I need in code chunks for the graphs to appear. I can solve this by including each chunk twice, with different options, as in ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= library(nlme) library(lattice) print(xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data)) @ but then, if I decide to change the plotting code, I have to make changes in two places. Is there some feature of Sweave or lattice I've missed that would simplify this? Re-use of code chunks doesn't seem to apply here. I usually use this variant of Duncan's suggestion: ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= plot(trellis.last.object()) @ -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave: infelicities with lattice graphics
On Sun, Sep 12, 2010 at 8:47 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 12/09/2010 11:41 AM, Michael Friendly wrote: Just a follow-up on this thread, now with R 2.11.1. I was happy back then to use Deepayan's solution for this, under earlier R versions; but it now gives an error and the Sweave-generated .tex file no longer compiles. ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= plot(trellis.last.object()) @ Now, I get the following from Sweave: Error: chunk 46 (label=ortho-xyplot1) Error in !lattice.getStatus(current.plot.saved, prefix = prefix) : invalid argument type Did something in lattice change so that plot(trellis.last.object()) no longer works or needs to be specified differently? I don't know if something in lattice has changed, but that doesn't look as though it should work: the code to do the plot was never evaluated. I think you would need eval=TRUE in the first chunk, or ortho-xyplot1-code ahead of the plot command in the second. Yes. I notice that it was me who introduced the eval=FALSE (I'm not sure why). Hopefully that should fix it. However, there _has_ been a recent lattice update, where the internals have undergone some change, so there is a chance that is to blame. I won't be able to take a look before day after tomorrow. -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave: infelicities with lattice graphics
Thanks Deepayan and Duncan. The eval=FALSE was the problem, rather than anything with lattice. Not sure why that worked earlier, but I no longer care. -Michael Deepayan Sarkar wrote: On Sun, Sep 12, 2010 at 8:47 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 12/09/2010 11:41 AM, Michael Friendly wrote: Just a follow-up on this thread, now with R 2.11.1. I was happy back then to use Deepayan's solution for this, under earlier R versions; but it now gives an error and the Sweave-generated .tex file no longer compiles. ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= plot(trellis.last.object()) @ Now, I get the following from Sweave: Error: chunk 46 (label=ortho-xyplot1) Error in !lattice.getStatus(current.plot.saved, prefix = prefix) : invalid argument type Did something in lattice change so that plot(trellis.last.object()) no longer works or needs to be specified differently? I don't know if something in lattice has changed, but that doesn't look as though it should work: the code to do the plot was never evaluated. I think you would need eval=TRUE in the first chunk, or ortho-xyplot1-code ahead of the plot command in the second. Yes. I notice that it was me who introduced the eval=FALSE (I'm not sure why). Hopefully that should fix it. However, there _has_ been a recent lattice update, where the internals have undergone some change, so there is a chance that is to blame. I won't be able to take a look before day after tomorrow. -Deepayan -- Michael Friendly Email: frien...@yorku.ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Streethttp://datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sweave: infelicities with lattice graphics
In a paper I'm writing using Sweave, I make use of lattice graphics, but don't want to explicitly show (or explain) in the article text the print() wrapper I need in code chunks for the graphs to appear. I can solve this by including each chunk twice, with different options, as in ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= library(nlme) library(lattice) print(xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data)) @ but then, if I decide to change the plotting code, I have to make changes in two places. Is there some feature of Sweave or lattice I've missed that would simplify this? Re-use of code chunks doesn't seem to apply here. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave: infelicities with lattice graphics
On 15/07/2010 4:51 PM, Michael Friendly wrote: In a paper I'm writing using Sweave, I make use of lattice graphics, but don't want to explicitly show (or explain) in the article text the print() wrapper I need in code chunks for the graphs to appear. I can solve this by including each chunk twice, with different options, as in ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= library(nlme) library(lattice) print(xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data)) @ but then, if I decide to change the plotting code, I have to make changes in two places. Is there some feature of Sweave or lattice I've missed that would simplify this? Re-use of code chunks doesn't seem to apply here. If the lattice call is always last in the chunk, I believe this would work as a replacement for the second chunk: ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= ortho-xyplot1-code print(.Last.value) @ and then you'll only have to edit the first one. But I haven't tried this, so something might go wrong... Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave: infelicities with lattice graphics
Dear Michael, I know this situation from writing vignettes and I usually cheat a bit I redefine the functions along these lines: plotmap - function (...) print (hyperSpec:::plotmap (...)) (plotmap is a lattice-function for hyperSpec objects) plotmap can tehn be used without the print in the vignettes - this works fine for almost all cases. Only, if you have a structure that one of the redefined functions call another one of them, you get e.g. a pdf with 2 pages. Have a look at the vignettes and particularly the file vignettes.defs of package hyperSpec (https://r-forge.r-project.org/scm/viewvc.php/Vignettes/?root=hyperspec). BTW: I find it polite to mention that some definitions etc. are executed silently and where people can find it. Cheers, Claudia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave: infelicities with lattice graphics
I have wondered about this too. The approach I use isn't pretty but does
have a couple of advantages - there is only one set of code to run and I
have control over the figure size.
The first part of the code below is what is shown in the document (but not
run), and the second part actually runs the code and makes the plot.
no2hist, eval=FALSE=
hist(mydata$no2)
no2hist1, echo = FALSE, results=hide=
pdf(no2hist.pdf)
no2hist
dev.off()
@
\begin{figure}
\centering
\includegraphics[width=0.5\textwidth]{no2hist}
\caption{The caption.}
\label{fig:hist}
\end{figure}
I'd be interested to know if there are neater ways of doing this.
Regards,
David
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Re: [R] Sweave: infelicities with lattice graphics
Dear David,
you can use Gin:
\setkeys{Gin}{width=0.5\linewidth}
just before the chunk that actually produces the figure.
and, cool, I hadn't realized, that
fig = TRUE, echo = FALSE=
print (
chunk-with-lattice-function
)
@
works.
with {} inside the print there can be even more than one statement in
the chunk-with-lattice-function.
However, that's not a good idea. There may be surprises due to the
question how often the chunk-with-lattice-function is actually executed.
Claudia
I have wondered about this too. The approach I use isn't pretty but does
have a couple of advantages - there is only one set of code to run and I
have control over the figure size.
The first part of the code below is what is shown in the document (but not
run), and the second part actually runs the code and makes the plot.
no2hist, eval=FALSE=
hist(mydata$no2)
no2hist1, echo = FALSE, results=hide=
pdf(no2hist.pdf)
no2hist
dev.off()
@
\begin{figure}
\centering
\includegraphics[width=0.5\textwidth]{no2hist}
\caption{The caption.}
\label{fig:hist}
\end{figure}
I'd be interested to know if there are neater ways of doing this.
Regards,
David
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave: infelicities with lattice graphics
On Thu, Jul 15, 2010 at 1:51 PM, Michael Friendly frien...@yorku.ca wrote: In a paper I'm writing using Sweave, I make use of lattice graphics, but don't want to explicitly show (or explain) in the article text the print() wrapper I need in code chunks for the graphs to appear. I can solve this by including each chunk twice, with different options, as in ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= library(nlme) library(lattice) print(xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data)) @ but then, if I decide to change the plotting code, I have to make changes in two places. Is there some feature of Sweave or lattice I've missed that would simplify this? Re-use of code chunks doesn't seem to apply here. I usually use this variant of Duncan's suggestion: ortho-xyplot1-code, keep.source=TRUE, eval=FALSE= library(nlme) library(lattice) xyplot(distance ~ age|Sex, data=Orthodont, type='b', groups=Subject, pch=15:25, col=palette(), cex=1.3, main=Orthodont data) @ ortho-xyplot1,fig=TRUE, include=FALSE, echo=FALSE, width=6, height=6= plot(trellis.last.object()) @ -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
