Re: [R] Sweave and ggplot2
Dear Thierry, Your guess was correct. I was not aware that I needed print( ). It was not needed with plot( ). I have yet to try xyplot( ) but I suspect that the print( ) might be needed here as well. Thank you very much for your help. Cheers, Sorn "ONKELINX, Thierry" <[EMAIL PROTECTED]> 04/08/2008 06:02 PM To <[EMAIL PROTECTED]>, cc Subject RE: [R] Sweave and ggplot2 Dear Sorn, It's hard to guess what your problem is, as you don't provide any sample code. My guess is that the graphics are empty. Did you use print(qplot(...)) or just qplot(). The latter won't work. You need print(qplot(...)) HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens [EMAIL PROTECTED] Verzonden: maandag 4 augustus 2008 6:55 Aan: r-help@r-project.org Onderwerp: [R] Sweave and ggplot2 Hi all, I've been trying to run Sweave with R code embedded - using the ggplot2 package and in particular the qplot command. There appears to be a problem in Sweave not picking up that qplot is a function. Has anybody else tried to use qplot in Sweave and have you been successful? Any help would be very much appreciated. Kind Regards, Sorn Notice: This email and any attachments may contain information\ ...{{dropped:26}} __ 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 and ggplot2
Dear Sorn, It's hard to guess what your problem is, as you don't provide any sample code. My guess is that the graphics are empty. Did you use print(qplot(...)) or just qplot(). The latter won't work. You need print(qplot(...)) HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens [EMAIL PROTECTED] Verzonden: maandag 4 augustus 2008 6:55 Aan: r-help@r-project.org Onderwerp: [R] Sweave and ggplot2 Hi all, I've been trying to run Sweave with R code embedded - using the ggplot2 package and in particular the qplot command. There appears to be a problem in Sweave not picking up that qplot is a function. Has anybody else tried to use qplot in Sweave and have you been successful? Any help would be very much appreciated. Kind Regards, Sorn Notice: This email and any attachments may contain information\ ...{{dropped:10}} __ 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 and ggplot2
Hi Ken, > This might be a case of FAQ 7.22 since ggplot(2) like lattice depend on grid. > I would try wrapping the ggplot commands in a print statement. Yes, you're right. Replacing : <>= ggplot(d,aes(y=t,x=u)) + geom_point(colour=alpha('black', 0.05)) @ with : <>= print(ggplot(d,aes(y=t,x=u)) + geom_point(colour=alpha('black', 0.05))) @ made the whole thing work. Thanks a lot ! Julien -- Julien Barnier Groupe de recherche sur la socialisation ENS-LSH - Lyon, France __ 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 and ggplot2
Julien Barnier no-log.org> writes: > > Hi, > When I try this example at work, I got an error message during Sweave > which is close from something like "warning : semitransparency not > supported by this device". When I try at home (with the given > sessionInfo), I got no warning but in both the cases the result is the > same : an empty pdf file for the figure and an error during pdflatex > compilation. > > I've put online an example Rnw file and the almost empty pdf produced > here : > > http://dd.nozav.org/transferts/ > > Thanks in advance for any help. This might be a case of FAQ 7.22 since ggplot(2) like lattice depend on grid. I would try wrapping the ggplot commands in a print statement. HTH, ken __ 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 and ggplot2
Hi, First, thanks for your help and sorry for not following the posting guide by not giving more detailed informations and an easily reproducible example... > i) Despite its annoncment in fortune("mind_read"), the mind_read() > function is apparently not to be released in R 2.6.0, so that if > you could just follow the posting guide and give a reproducible > example... Well, I hope it will be ready for R 2.7.0 ! > ii) Give the output of your sessionInfo(). You can use something > like that in your *.rnw file: > > <>= > toLatex(sessionInfo()) > @ Here it is : , | R version 2.5.1 (2007-06-27) | i486-pc-linux-gnu | | locale: | [EMAIL PROTECTED];LC_NUMERIC=C;[EMAIL PROTECTED];[EMAIL PROTECTED]; | [EMAIL PROTECTED];[EMAIL PROTECTED];[EMAIL PROTECTED];LC_NAME=C; | LC_ADDRESS=C;LC_TELEPHONE=C;[EMAIL PROTECTED];LC_IDENTIFICATION=C | | attached base packages: | [1] "grDevices" "utils" "datasets" "graphics" "stats" "methods" | [7] "base" | | other attached packages: | car | "1.2-1" ` > iii) What do you mean exactly by "doesn't work"? Put the source and > the output somewhere on the web so that we can see both. "Doesn't work" means that the generated pdf file for the figure generated by the chunk is empty. It is not of size 0, but it has no content and so cannot be included when running pdflatex, which exits with an error : , | !pdfTeX error: pdflatex (file ./alpha_sweave-004.pdf): PDF inclusion: required | page does not exist <0> | ==> Fatal error occurred, no output PDF file produced! ` When I try this example at work, I got an error message during Sweave which is close from something like "warning : semitransparency not supported by this device". When I try at home (with the given sessionInfo), I got no warning but in both the cases the result is the same : an empty pdf file for the figure and an error during pdflatex compilation. I've put online an example Rnw file and the almost empty pdf produced here : http://dd.nozav.org/transferts/ Thanks in advance for any help. -- Julien __ 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 and ggplot2
Dear Julien, > Hi, > > I am trying to use ggplot2 graphics with Sweave, but I got problems > with transparency support when generating pdf figures, even if I > specify a ?pdf.version? argument in Sweave options. > [...snip...] I wanted to help because I'm interested by the exploitation of the alpha channel in Sweave documents too... However, i) Despite its annoncment in fortune("mind_read"), the mind_read() function is apparently not to be released in R 2.6.0, so that if you could just follow the posting guide and give a reproducible example... ii) Give the output of your sessionInfo(). You can use something like that in your *.rnw file: <>= toLatex(sessionInfo()) @ iii) What do you mean exactly by "doesn't work"? Put the source and the output somewhere on the web so that we can see both. Sincerely, -- Jean R. Lobry([EMAIL PROTECTED]) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I, 43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE allo : +33 472 43 27 56 fax: +33 472 43 13 88 http://pbil.univ-lyon1.fr/members/lobry/ __ 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.