Dear Tena, As I am a WinXP user I have no expercience with Linux. I would suggest you try the plot on a pdf device. pdf does support transparancy (at least on windows and for pdf version >= 1.4). HTH, Thierry
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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 thierry.onkel...@inbo.be 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 ________________________________ Van: Tena Sakai [mailto:tsa...@gallo.ucsf.edu] Verzonden: donderdag 7 mei 2009 18:13 Aan: ONKELINX, Thierry; Ian Fellows; r-help@r-project.org Onderwerp: RE: [R] I updated/reinstalled ggplot2 and the trouble started... Hi, > What device are you using to plot the graph? I am not explicitly specifying any. I am on redhat linux and as I understand it R uses DISPLAY environment variable, which is set for an X11 server (X Darwin, v1.4.0, X11 6.8.2). Other qplot()'s I have used (straight out of the book) work fine. I am coming to believe that before the current incarnation, it simply ignored the alpha parameter and gave the plot, whereas with the latest it doens't want to ignore and not going further. I'd be curious if this problem is reproducible with anybody else. Regards, Tena Sakaki tsa...@gallo.ucsf.edu -----Original Message----- From: ONKELINX, Thierry [mailto:thierry.onkel...@inbo.be] Sent: Thu 5/7/2009 1:01 AM To: Tena Sakai; Ian Fellows; r-help@r-project.org Subject: RE: [R] I updated/reinstalled ggplot2 and the trouble started... What device are you using to plot the graph? According to the warning, the device is causing the problem. 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 thierry.onkel...@inbo.be 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: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Tena Sakai Verzonden: donderdag 7 mei 2009 6:22 Aan: Ian Fellows; r-help@r-project.org Onderwerp: Re: [R] I updated/reinstalled ggplot2 and the trouble started... Hi Ian, Per your suggestion, I reinstalled R 2.9.0, then I reinstalled ggplot2 on top. The problem persists. Here's the what happens after the installation: > qplot (carat, price, data = diamonds, alpha = I(1/10)) Warning message: In grid.Call.graphics("L_points", x$x, x$y, x$pch, x$size) : semi-transparency is not supported on this device: reported only once per page The entire record of installing ggplot2 package, ending up with the line above is in the attached file. I would think this should be reproducible with anybody else. If you have any other suggestion, I am all ears. Regards, Tena Sakai tsa...@gallo.ucsf.edu -----Original Message----- From: Ian Fellows [mailto:ifell...@gmail.com] Sent: Tue 5/5/2009 11:43 PM To: Tena Sakai Subject: Re: I updated/reinstalled ggplot2 and the trouble started... Tena, May I suggest that you do a full clean install of R 2.9.0, then install ggplot2 from cran. See if the problem persists after that. Ian On Tue, May 5, 2009 at 11:13 PM, tena <tsa...@gallo.ucsf.edu> wrote: > > Hi Hadley, > > Many thanks for your reply. > > I followed your instruction and got past the point where I > was stuck at. Namely, I was able to generate a few plots. > But as I came to the second half of section 2.4, where I > wanted to see the behavior of alpha paramter, which I > had apparently misspelled, I encountered another hindrance: > > qplot (carat, price, data = diamonds, alpha = I(1/10)) > Warning message: > In grid.Call.graphics("L_points", x$x, x$y, x$pch, x$size) : > semi-transparency is not supported on this device: reported only > once per page > > A plot was generated, but there are tic marks and labels on > each direction, but no plot at all. > > I wonder if this is yet another (hidden) package to be updated... > The warning message suggests grid, but I am hesitant to do > something without knowing what is what. I would appreciate > your instruction. > > Regards, > > Tena Sakai > > > On May 5, 5:24 pm, hadley wickham <h.wick...@gmail.com> wrote: > > Hi Tena, > > > > R isn't very good at detecting when package dependencies also need to > > be updated, so you probably need to do: > > > > install.packages(c("reshape","plyr")) > > > > And you want > > > > qplot (carat, price, data=diamonds, alpha = I(1/10)) > > > > not > > > > qplot (carat, price, data=diamonds, slpha = i(1/10)) > > > > Hadley > > > > On Tue, May 5, 2009 at 6:27 PM, tena <tsa...@gallo.ucsf.edu> wrote: > > > > > Hi Folks, > > > > > I am pretty new to R and I am even newer to ggplot. > > > > > I am using R 2.7.1, 2.8.1, and 2.9.0 on linux host and > > > what I am experiencing holds for all three. > > > > > I was just typing a few examples from the chapter 2 of > > > the book, ggplot2 --Elegant graphics for data analysis. > > > > > I typed 3 qplot lines on page 13: > > > > qplot (carat, price, data=diamonds, slpha = i(1/10)) > > > > qplot (carat, price, data=diamonds, slpha = i(1/100)) > > > > qplot (carat, price, data=diamonds, slpha = i(1/200)) > > > > > To me, the plot looked identical. I went to my R library > > > directory and looked at the date on the ggplot2 directory, > > > which was April of 2008. I decided to update the library. > > > In R, I issued: > > > > install.packages ('ggplot2', '/usr/local/Gallo/R') > > > and there was a complaint as to permission denied for > > > saving the current version (or something). I reissued > > > the command as root and this time it gave me a normal > > > return. > > > > > I was ready to retrace my steps with the book. I only got > > > to page 11 this time. Here's what happened (in all three > > > versions): > > > > set.seed (1410) > > > > dsmall <- diamonds [sample (nrow(diamonds), 100), ] > > > > > > > > qplot (carat, price, data = diamonds) > > > Error in get("new", env = FacetGrid, inherits = TRUE) > > > (FacetGrid, ...) : > > > could not find function "is.formula" > > > > > > > > > Can somebody please clue me in as to what's happening, > > > what I am doing wrong, etc? > > > > > Regards, > > > > > Tena Sakai > > > tsa...@gallo.ucsf.edu > > > > --http://had.co.nz/ > --~--~---------~--~----~------------~-------~--~----~ > You received this message because you are subscribed to the ggplot2 mailing > list. > To post to this group, send email to ggpl...@googlegroups.com > To unsubscribe from this group, send email to > ggplot2+unsubscr...@googlegroups.com<ggplot2%2bunsubscr...@googlegroups. com> > For more options, visit this group at > http://groups.google.com/group/ggplot2 > -~----------~----~----~----~------~----~------~--~--- > > Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. [[alternative HTML version deleted]] ______________________________________________ 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.
