On Nov 9, 2011, at 4:22 PM, Cynthia Lee Page wrote:
Hi R people!
I have a directory of .csv files I would like to make into objects
then scatter plots. I have been having varying degrees of progress.
I was able
make an object of all files, loop through it, and make a pdf of the
last file I looped through. I kept renaming the pdf so instead of
ending up with
27 pdfs I got one, with the data from the last file
I have been tweaking with it and now can't even make the data object
and I am not sure why.
I am a bit brain dead at this point :)
I am new to R and have been programming in perl - but not all that
long
Could you please have al look at it..
here is the script I have been using
# source of this code below
#http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_scrpt.html
# store the current directory
initial.dir<-getwd()
# change to the new directory
setwd("/data/homes/ccpage/ngs/Argueso/Tophat/flocculated/cuffdiff/
fpkmgt")
# source of this code below
# https://stat.ethz.ch/pipermail/r-help/2008-March/158336.html
files <- Sys.glob("*.csv") # get names of files to process
#result <- numeric(length(files)) # preallocate assuming single
value from each file
for (i in seq_along(files)){
# want to give each object a unique name would like to use file[i]
MINUS the .csv extention regex
#test<-files[i] # tried to use as variable to name each pdf this
object is the name of last file in loop
data <- read.csv(files[i])
# I want to name the pdf the same name as the object with a .pdf
extention here I think it will be file[i].csv.pdf
# I don't know how to use regex in R I could
readLines(objectnames.txt) and loop through those as well
pdf("data.pdf")
At this point you might have been better off if you had just typed:
pdf()
The default name for a pdf document is set by this code from the help
page for pdf()
pdf(file = ifelse(onefile, "Rplots.pdf", "Rplot%03d.pdf"),
Notice that "%03d". That means the system pots in a number tthat is
one grater than the largest current Rplot_N.pdf in the directory.
plot(data$fpkma,data$fpkmb, main="Scatter plot of
data",xlab="FPKM of First Time Point",ylab="FPKM of Second Time
Point")
dev.off()
}
# change back to the original directory
setwd(initial.dir)
############################################################
the command I have been using :
R CMD BATCH /data/homes/ccpage/ngs/rscripts/test_for.R
The Rout
> # source of this code below
> #http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_scrpt.html
>
> # store the current directory
> initial.dir<-getwd()
> # change to the new directory
> setwd("/data/homes/ccpage/ngs/Argueso/Tophat/flocculated/cuffdiff/
fpkmgt")
>
> # source of this code below
> # https://stat.ethz.ch/pipermail/r-help/2008-March/158336.html
>
> files <- Sys.glob("*.csv") # get names of files to process
> #result <- numeric(length(files)) # preallocate assuming single
value from each file
>
> for (i in seq_along(files)){
+ # want to give each object a unique name would like to use file[i]
MINUS the .csv extention regex
+ #test<-files[i] # tried to use as variable to name each pdf this
object is the name of last file
+
+ data <- read.csv(files[i])
+
+ # I want to name the pdf the same name as the object with a .pdf
extention here I think it will be file[i].csv.pdf
+ # I don't know how to use regex in R I could
readLines(objectnames.txt) and loop through those as well
+
+ pdf("data.pdf")
+ plot(data$fpkma,data$fpkmb,main="Scatter plot of
data",xlab="FPKM of First Time Point",ylab="FPKM of Second Time
Point")
+ dev.off()
+ }
Error in plot.window(...) : need finite 'xlim' values
Without the data that created that error, we are not going to be able
to give a clear answer.
Calls: plot -> plot.default -> localWindow -> plot.window
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
Execution halted
Thanks for any help!\
David Winsemius, MD
West Hartford, CT
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