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

From: "Thomas S. Dye" <tsd@tsdye.com>
To: Dan Davison <dandavison7@gmail.com>
Cc: emacs-orgmode@gnu.org
Subject: Re: Re: [babel] R: New handling of file output
Date: Sat, 1 Jan 2011 12:58:43 -1000	[thread overview]
Message-ID: <30A86C75-D89E-45F4-A482-C81218CECAD9@tsdye.com> (raw)
In-Reply-To: <m1hbe7dpx1.fsf@94.196.16.201.threembb.co.uk>

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

#+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
>>
>>
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>
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