Re: [babel] R: New handling of file output

From: Dan Davison <dandavison7@gmail.com>
To: emacs-orgmode@gnu.org
Subject: Re: [babel] R: New handling of file output
Date: Thu, 06 Jan 2011 17:14:14 +0000	[thread overview]
Message-ID: <m162u2ymxl.fsf@94.196.59.243.threembb.co.uk> (raw)
In-Reply-To: 30A86C75-D89E-45F4-A482-C81218CECAD9@tsdye.com

"Thomas S. Dye" <tsd@tsdye.com> writes:

> Aloha all,
>
> Here is an example of the new handling of file output with an R source  
> code block that doesn't use "base" graphics:
>
> #+srcname: r-edge-angle-histogram
> #+begin_src R :results output graphics :var x=whole-adzes :file r/ 
> adze_edge_angle.png :width 400 :height 300
>    library(ggplot2)
>    adze.edge.angle <- ggplot(x, aes(edge_angle))
>    adze.edge.angle + geom_histogram(aes(y=..density..)) +
>    geom_density(weight=2) + xlab("Measured cutting edge angle  
> (degrees)")
> #+end_src

I was initially a bit baffled by this example. If anyone else is curious
as to why, when graphics are generated by ggplot2, :results output is
required in addition to :results graphics, please see Erik Iverson's
original post on producing grid-based (e.g. lattice, ggplot2) R graphics
with org-babel (bearing in mind of course that the header arg syntax has
changed as per this thread).

http://article.gmane.org/gmane.emacs.orgmode/26082

Dan

>
> #+results:
> [[file:r/adze_edge_angle.png]]
>
> Previously, the source line was:
> #+begin_src R :results output :var x=whole-adzes :file r/ 
> adze_edge_angle.png :width 400 :height 300
>
> The only change was to append graphics to :results output.
>
> All the best,
> Tom
>
> On Dec 21, 2010, at 6:57 AM, Dan Davison wrote:
>
>> Dan Davison <dandavison7@gmail.com> writes:
>>
>>> Please note the following changes to the way that org-babel handles
>>> file output. These may break existing org-babel files which use
>>> the :file header argument.
>>>
>>> :file <filename> should be understood as saying "write the result
>>> to <filename> and return a link to <filename>".
>>>
>>> This works for all languages. For graphics languages (e.g. ditaa,  
>>> dot,
>>> gnuplot) there is no change in behavior: "result" in the above is the
>>> graphics, and a link to the image is placed in the org buffer. For
>>> general-purpose languages (e.g. emacs-lisp, python, R, ruby, shell),
>>> the "result" written to file is the normal org-babel result (string,
>>> number, table).
>>>
>>> This is a backwards-incompatible change for R, which was previously
>>> interpreting :file to mean "send graphics to file". I will send a
>>> separate email concerning R.
>>
>> Previously R understood :file <filename> to mean "save graphics to
>> <filename>"[1]; now R behaves like other languages and sends the  
>> normal
>> org-babel result to file (string, number, table). To tell R to save
>> graphics[1] to file, use :results graphics.
>>
>> Some examples:
>>
>> Wrong!
>>
>> #+begin_src R :file img.png
>> hist(rnorm(100))
>> "img.png is going to contain this string."
>> #+end_src
>>
>> Use :results graphics save graphics:
>>
>> #+begin_src R :file img.png :results graphics
>> hist(rnorm(100))
>> "But now img.png is going to contain graphics."
>> #+end_src
>>
>> You may want to use `org-babel-default-header-args:R' to make this
>> more convenient:
>>
>> #+begin_src emacs-lisp
>>  (setq org-babel-default-header-args:R
>>        '((:results . "graphics")))
>> #+end_src
>>
>> Alternatively the :results graphics header can be set in a property
>> drawer for the subtree, or a #+babel: line, as usual.
>>
>> Now this will do what was intended
>> #+begin_src R :file img.png
>> hist(rnorm(100))
>> #+end_src
>>
>> Here is an example of saving something other than base graphics to  
>> file,
>> and returning a link to the file. Note that :file is not used, and the
>> filename must be returned. This could be used to save images created  
>> by
>> non-base graphics libraries:
>>
>> #+begin_src R :results file :var file="savefile"
>> write.something.to.file <- function(f) cat("hello", file=f)
>> write.something.to.file(f=file)
>> file
>> #+end_src
>>
>>
>> Dan
>>
>>
>> * Footnotes
>> [1] This only works for "base" graphics.
>>
>>
>>
>>>
>>> In order to return a file link from a src block without telling babel
>>> to save any results to that file, use :results <filename> and do not
>>> use :file. The code block can of course write arbitrary content to
>>> <filename>.
>>>
>>> Some examples:
>>>
>>> Save the output of ls -l as a .csv file (recall that :results value  
>>> is
>>> the default):
>>>
>>> #+begin_src sh :file dirlisting.csv :sep ,
>>> ls -l
>>> #+end_src
>>>
>>> Send the text output of ls -l directly to file:
>>>
>>> #+begin_src sh :results output :file dirlisting.txt
>>> ls -l
>>> #+end_src
>>>
>>> Dan
>>>
>>>
>>> _______________________________________________
>>> Emacs-orgmode mailing list
>>> Please use `Reply All' to send replies to the list.
>>> Emacs-orgmode@gnu.org
>>> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>>
>>
>> _______________________________________________
>> Emacs-orgmode mailing list
>> Please use `Reply All' to send replies to the list.
>> Emacs-orgmode@gnu.org
>> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Please use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode