Thanks all for the solutions provided! Mannie and Joe, the tiff() or png() or jpeg() works well. But the use of "useDingbats=F" suggested by Erik looks a bit better since it uses vector instead of pixel graphic.
Matthew -----Original Message----- From: Standing Joseph (GREAT ORMOND STREET HOSPITAL FOR CHILDREN NHS FOUNDATION TRUST) [mailto:[email protected]] Sent: Friday, November 20, 2015 8:24 PM To: Kajsa Harling <[email protected]>; HUI, Ka Ho <[email protected]>; [email protected] Subject: RE: [NMusers] Incomplete circles drawn in VPC plotted using R scripts generated by PsN I think it is a problem with R making pdfs. Workaround: try using tiff() or png() instead - then you can save the image as a pdf. Joe ________________________________________ From: [email protected] [[email protected]] On Behalf Of Kajsa Harling [[email protected]] Sent: 20 November 2015 10:33 To: HUI, Ka Ho; [email protected] Subject: Re: [NMusers] Incomplete circles drawn in VPC plotted using R scripts generated by PsN Dear Matthew, I suggest you consult the xpose.VPC documentation ( ?xpose.VPC() ) for instructions on how to change how values are marked in the plot. The PsN -rplots script uses the default settings. Best regards, Kajsa On 11/19/2015 03:56 PM, HUI, Ka Ho wrote: Dear all, I was trying to generate VPC using the R scripts generated by PsN with the following command line: vpc -samples=200 -stratify_on=... -rplots=1 -idv=TIME -auto_bin=unique -predcorr -varcorr -dir=vpc_FINAL_MODEL FINAL_MODEL_vpc.mod The R script generated looks like this: #START OF AUTO-GENERATED PREAMBLE, WILL BE OVERWRITTEN WHEN THIS FILE IS USED AS A TEMPLATE #Created 2015-11-19 at 22:05 rplots.level <- 1 xpose.runno <- '1_vpc' toolname <- 'vpc' pdf.filename <- paste0('PsN_',toolname,'_plots.pdf') pdf.title <- 'vpc diagnostic plots run 1_vpc' working.directory<-'C:/...' raw.results.file <- 'raw_results_FINAL_MODEL1_vpc.csv' model.directory<-'C:/...' model.filename<-'FINAL_MODEL1_vpc.mod' subset.variable<-NULL mod.suffix <- '.mod' mod.prefix <- 'FINAL_MODEL' tab.suffix <- '' tool.results.file <- 'vpc_results.csv' theta.labels <- c('T1','T2','T3','T4','T5','T6') theta.fixed <- c(FALSE,FALSE,TRUE,FALSE,FALSE,FALSE) omega.labels <- c('O1','O2') omega.fixed <- c(FALSE,FALSE) sigma.labels <- c('S1') sigma.fixed <- c(FALSE) n.eta <- 2 n.eps <- 1 vpctab <- 'vpctab' have.loq.data <- FALSE have.censored <- FALSE is.categorical <- FALSE is.tte <- FALSE dv <- 'DV' idv <- 'TIME2' setwd(working.directory) ############################################################################ #END OF AUTO-GENERATED PREAMBLE #WHEN THIS FILE IS USED AS A TEMPLATE THIS LINE MUST LOOK EXACTLY LIKE THIS library(xpose4) pdf(file=pdf.filename,width=10,height=7,title=pdf.title) done <- FALSE if (is.tte){ #data is in the model directory, go there to read input setwd(model.directory) xpdb <- xpose.data(xpose.runno) plots <- kaplan.plot(object=xpdb,VPC=T) #go back to vpc directory setwd(working.directory) done <- TRUE } if (is.categorical & (!done)){ plots<-xpose.VPC.categorical(vpc.info=tool.results.file,vpctab=vpctab) done <- TRUE } if ((have.loq.data | have.censored) & (!done) ){ plots<-xpose.VPC.both(vpc.info=tool.results.file,vpctab=vpctab) done <- TRUE } if (!done){ plots<-xpose.VPC(vpc.info=tool.results.file,vpctab=vpctab) done <- TRUE } print(plots) dev.off() However the "circles" (indicating raw Cp data) are incomplete and take the shape of a "crescent moon" instead. When run with the -lloq option, the 1st stratification has complete circles but the remaining 2 also has the crescent-moon circles instead. Other parts of the plots (Shades and plots of CI) look normal. Can anyone suggest any possible cause and solution? Thanks and regards, Matthew Hui -- ----------------------------------------------------------------- Kajsa Harling, PhD System Developer Department of Pharmaceutical Biosciences Uppsala University [email protected]<mailto:[email protected]> +46-(0)18-471 4308 http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/ ----------------------------------------------------------------- ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ********************************************************************************************************************
