R help - Nov 2011 - R to automate scatter plots

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")
     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
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!

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

It's usually encouraged to reply to the list as well for
threading/archive reasons. (And because occasionally your first
respondent will say something wrong and require correction -- I was
called out just this morning...oops)

Yes, you seem to be using it right to add a title to the plot but you
have a few syntactical errors (one of which I think came from my first
reply): I think you would prefer this:

paste(data$fpkma, data$pdkmb, main paste(substr(files[i],1,nchar(files[i])-4),
".pdf", collapse = ""),
xlab = "FPKM First", ylab = "FPKM Second")

The placement of pdf() is irrelevant to how you get the names: whether
you put it outside or inside the loop, you can still either name it
directly by adding an argument to pdf() or use the default behavior:
the placement only affects whether you want one pdf with all your
plots or multiple pdfs of one plot each. The only other thing is that
you should call pdf() before plot() to make sure the pdf is ready to
take the plot.

Michael

On Thu, Nov 10, 2011 at 11:20 AM, Cynthia Lee Page
<Cynthia.Page at colorado.edu> wrote:
> HI Michael,
>
> You are exactly right about the object data. In my tweaking I messed up all
> my .csv and they were no longer .csv's
> So there was ?no data object.
>
> I will try what you suggested regarding generating the pdf files and naming
> them. I think I can use the same technique to
> add a title to each plot I am not sure if I can use paste(
> substr(files[i],1, nchar(files[i]-4)), ".pdf" below in the plot
title as:
>
> plot(data$fpkma, data$fpkmb, main=paste( substr(files[i],1,
> nchar(files[i]-4)), ".pdf", xlab = "FPKM First",
ylab="FPKM Second")
>
> but I will try it.
>
> ?If I put the pdf() outside the loop the plots may go directly to
Rplot.pdf.
> I think I have to call pdf() before calling plot() inorder to customize the
> name.
>
> Now I am ramblin!
>
> One other thing. I have been responding via reply to sender directly to
> those who have responded to me ?- I have not posted ?to the list.
>
> Should I be?
>
> Thanks so much,
>
> Cynthia
>
>
>
> On Nov 9, 2011, at 6:28 PM, R. Michael Weylandt wrote:
>
>> It sounds like something is going wrong in your data read -- the
>> warnings indicate that R probably isn't 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
>>>
>>> ______________________________________________
>>> R-help at 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.
>>>
>
>

I think you are off in the order of calls: you need to open the pdf
and then do all the plots so that they get pushed to the pdf. The
blank plot call won't do anything particularly helpful. If you use
pdf() after most of the plot commands they go to your default device
which is usually printing to the screen -- it's not tricky to copy a
plot from another device to a pdf, but you need to use dev.copy2pdf()
to do so.

Try this

pdf("test.pdf") # Open the pdf driver
plot(1:5) # Put one plot on the pdf
plot(1:6, col = 2) # put a seonc plot on the pdf
dev.off() # close the pdf

On my machine this produces a pdf with two plots.

For your script

pdf()

forloop

dev.off()



On Thu, Nov 10, 2011 at 2:38 PM, Cynthia Lee Page
<Cynthia.Page at colorado.edu> wrote:
> Michael,
>
> Thanks for all your help.
>
> I have things working pretty nicely now and will post back to my thread
> incase
> any one else needs a solution or has something to add but before I do I
want
> to
> understand how to print all plots to one pdf.
>
> So far this is not working for me. If I make a new pdf("all.pdf")
> after the for loop, and then repeat the plot command, followed by a
> dev.off(),
> ie
> for () {
> # ?all the individual pdfs here
> }
> pdf("allpdf")
> plot()
> devoff.()
>
> I only get one page on the all.pdf with the plot of the last data object,
so
> again it is writing over the last pdf
>
> Cynthia
>
>
> On Nov 10, 2011, at 11:48 AM, R. Michael Weylandt wrote:
>
>> It's usually encouraged to reply to the list as well for
>> threading/archive reasons. (And because occasionally your first
>> respondent will say something wrong and require correction -- I was
>> called out just this morning...oops)
>>
>> Yes, you seem to be using it right to add a title to the plot but you
>> have a few syntactical errors (one of which I think came from my first
>> reply): I think you would prefer this:
>>
>> paste(data$fpkma, data$pdkmb, main >>
paste(substr(files[i],1,nchar(files[i])-4), ".pdf", collapse =
""),
>> xlab = "FPKM First", ylab = "FPKM Second")
>>
>> The placement of pdf() is irrelevant to how you get the names: whether
>> you put it outside or inside the loop, you can still either name it
>> directly by adding an argument to pdf() or use the default behavior:
>> the placement only affects whether you want one pdf with all your
>> plots or multiple pdfs of one plot each. The only other thing is that
>> you should call pdf() before plot() to make sure the pdf is ready to
>> take the plot.
>>
>> Michael
>>
>> On Thu, Nov 10, 2011 at 11:20 AM, Cynthia Lee Page
>> <Cynthia.Page at colorado.edu> wrote:
>>>
>>> HI Michael,
>>>
>>> You are exactly right about the object data. In my tweaking I
messed up
>>> all
>>> my .csv and they were no longer .csv's
>>> So there was ?no data object.
>>>
>>> I will try what you suggested regarding generating the pdf files
and
>>> naming
>>> them. I think I can use the same technique to
>>> add a title to each plot I am not sure if I can use paste(
>>> substr(files[i],1, nchar(files[i]-4)), ".pdf" below in
the plot title as:
>>>
>>> plot(data$fpkma, data$fpkmb, main=paste( substr(files[i],1,
>>> nchar(files[i]-4)), ".pdf", xlab = "FPKM
First", ylab="FPKM Second")
>>>
>>> but I will try it.
>>>
>>> ?If I put the pdf() outside the loop the plots may go directly to
>>> Rplot.pdf.
>>> I think I have to call pdf() before calling plot() inorder to
customize
>>> the
>>> name.
>>>
>>> Now I am ramblin!
>>>
>>> One other thing. I have been responding via reply to sender
directly to
>>> those who have responded to me ?- I have not posted ?to the list.
>>>
>>> Should I be?
>>>
>>> Thanks so much,
>>>
>>> Cynthia
>>>
>>>
>>>
>>> On Nov 9, 2011, at 6:28 PM, R. Michael Weylandt wrote:
>>>
>>>> It sounds like something is going wrong in your data read --
the
>>>> warnings indicate that R probably isn't 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
>>>>>
>>>>> ______________________________________________
>>>>> R-help at 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.
>>>>>
>>>
>>>
>
>