similar to: R command line arguments

Again me. I want to plot the numbers on the bars of a barplot. This can be done using hist function when setting the label argument true (i.e. data <- c(1,2,3,4) hist(data, labels=T) When I try this using barplot I get an error: > barplot(summary(data), labels=T) Error in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty, : formal

Sorry for the question, but I really cannot find the right search terms to find an answer.. I have a data frame with strings in some of the columns. I want to know all the rows where the strings in both columns are equal. How do I do this? Thanks, Bernd [[alternative HTML version deleted]]

Hi, I am new to R and couldn't find any information on how to handle my table data that I just read in the way I want to use it.. I read in a table from a file: x <- read.delim("filenam", header=TRUE) one column (x$label) hold the class labels. Another holds some values (x$val). I want to calculate summary statistics for different classes. How would I do this? Thanks, Bernd

Hi there, I want to run an R script on a cluster with qsub. Obviously I don't want to display any X window, but I want use png() or something else to write out images. Unfortunately I get the following error message: > png(filename = " ALL.png", width = 480, height = 480, pointsize = 12, bg = "white", res = NA) Error in X11(paste("png::", filename,

Hi, I have a bunch of R scripts which have the hash bang !/usr/bin/env Rscript and I typically run these scripts by passing in some parameters like this: ./nameOfRScript arg1 arg2 ... I know Rscript has the option to run in --vanilla. Where exactly do I insert the --vanilla option? When I do something like this: ./nameOfRScript --vanilla arg1 arg2 ... And I try to access the commandArgs,

Hello and sorry to bother. Please help. I searched the archives but could not find out why --args is being ignored on Windows 2000. I try R CMD BATCH --slave 11.R 11.Rout --args "12" and 11.R has x=commandArgs(trail=T) print(x) a=x[length(x)] write.csv(a,file="13.out") q("no") the argument is not passed to the R process. 11.Rout only shows processing time and

Hi, I have a few hundreds files with numerical information of different length but with the same column structure. I use the following code to get summary statistics fplist <- list.files(pattern=".*analysis") for (fp in fplist){ x2 <- read.delim(fp) summary(x2) } Summary gives something like: summary (x2) V1 V2

Hi, $ cat commandArgs.R args=commandArgs(trailingOnly=TRUE) args[1]+10 I have the above code. But the following command line gives me an error. I am wondering what is the correct way to convert a string to a vector? $ Rscript commandArgs.R 1:3 > args=commandArgs(trailingOnly=TRUE) > args[1]+10 Error in args[1] + 10 : non-numeric argument to binary operator Execution halted Regards, Peng

I am trying split a string and use one part of it to label graphs. I am using strsplit for that. While I am able to split it, how do I access the separated parts. > filName<-"chrI_2223" >part<- strsplit(filName,"\\_") > part [[1]] [1] "chrI" "2223" > part[1] [[1]] [1] "chrI" "2223" I looked up the help archive but did

I think there's a minor bug in the argument-processing carried out by Rscript. The effect is that if one passes "-g" as a flag to the script, it is erroneously exposed to the main executable's argument processing and therefore generates a message about not being able to comply with the request for a particular GUI. Uppercase G is fine as are the other 25 letters in upper or

Apologies for asking about this, but I don't quite understand how this works after looking through the FAQ and the Help archives. Let's say I want to pass "1000" as an argument to R. I did the following: >R CMD BATCH --1000 infile outfile When I do print( commandArgs() ), I see [1] ".../R.bin" "--restore" [3] "--save"

Hi there, I am looking for R-packages that can help me visualize properties on nucleotide sequences. I want to display sequences in the 1-100K base range as lines and plot features above and below those lines. Any ideas would be welcome. Thanks, Bernd

Dear R experts: I am a bit stymied by how the argument picking-off works in R batch file usage. $ cat commandArgs.R cat(" Command Line Arguments were ", commandArgs(), "\n"); $ /usr/bin/R CMD BATCH commandArgs.R --args 1 2 3 $ /usr/bin/R --args 1 CMD BATCH commandArgs.R ... I am now getting into interactive mode ?! I guess it really is skipping the rest of the command line

Hi all, I am setting up some R program files for use by our DB programmers to enable them to utilize some R functions which will be called from within TCL code. R has been installed on an RHEL server and R will process the results of SQL queries against an Oracle database. In some cases, they will generate a data file to be read in and processed by R, in others they will simply make the

Hello list Is there a way of identifying from within R whether a script has been source(d) from Rgui.exe or via Rscript.exe in batch mode? For the code I have I use the commandArgs() function to pick up command line args when running in batch mode via Rscript.exe However I like to get the code working manually first using source("MyRCode.r") I'd like to be able to put something at

I have the following script (also attached): #!/usr/bin/Rscript spec=matrix(c( 'verbose', 'v', 1, "integer", 'help' , 'h', 0, "logical" ),ncol=4, byrow=TRUE) spec.dim=dim(spec) spec.opt.long=spec[,1] spec.opt.short=spec[,2] spec.opt.l <- spec.dim[1] infile <- "test.dat" args=commandArgs(TRUE); l=length(args) self =

Hi Guys I am Abhishek, primarily a bioinformatician. I have recently started using a lot of R thanks to some excellent packages available. Lately I have felt the need to batch process few of the R scripts I have been working with and strangely enough I am not able to find a good resource on how to best do this. I did find few old threads on the archives but none convinced me much. So here I am

A couple of weeks ago I asked how it is possible to run an R script (not a function) passing some parameters. Someone suggested the function "commandArgs()". I read the on-line help and found no clarifying example. Therefore I do not know how to use it appropriately. I noticed this function returns the pathname of the R executable which is not what I need. I meant to ask if it is

Hi, The problem is most likely, you need to call a R CMD BATCH with your arguments and the R-script inside of a shell script that you submit to your qsub. Unfortunately we don't use qsub anymore so can't test it, but it should be as follows: R-script eg. test.R: > ##First read in the arguments listed at the command line > args=(commandArgs(TRUE)) > > ##args is now a list of

Dear R experts This probably seems very easy to you guys, but I'm a beginner and would be really glad if someone helped me with this: I am trying to automate the execution of an R script (let's call it "myscript.R") by passing a variable from a bash script to myscript.R. I know I can use the command Rscript, but I don't know how to declare in bash which variable will be