[R] R to automate scatter plots

[R. Michael Weylandt]

Sorry for the rambling answer:

On Wed, Nov 9, 2011 at 8:28 PM, R. Michael Weylandt
<michael.weylandt at gmail.com> wrote:
> It sounds like something is going wrong in your data read -- the
> warnings indicate that R probably isn't data**

meant to say: getting numerical data.

>  to the plotting commands.
> My totally off the wall guess is that if your data is coming by way of
> excel, the commas are leading to your data becoming characters and
> hence not plotting nicely, but that's just a guess. add browser()
> inside your loop between the read commands and the plot just to see
> what your data actually looks like inside R and try to track down the
> error.
>
> As to your pdf() question -- you can also just put it outside the loop
> and close dev.off() after the loop. Then all your plots will be in one
> pdf. Though, perhaps this is what you were looking for as far as name
> manipulation:
>
> pdf(file = paste( substr(files[i],1, nchar(files[i]-4)), ".pdf", sep = "")
>
> Michael
>
> On Wed, Nov 9, 2011 at 5:32 PM, David Winsemius <dwinsemius at comcast.net> wrote:
>>
>> 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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>