From: Joseph Cole <coljo582@student.otago.ac.nz>
To: davison@stats.ox.ac.uk, Emacs-orgmode@gnu.org
Subject: Re: Org babel R Help
Date: Sun, 21 Mar 2010 22:18:48 +1300 [thread overview]
Message-ID: <20100321221848.100245krd2ozqirc@www.studentmail.otago.ac.nz> (raw)
In-Reply-To: <5084fc611003210151x41850afcg36b275679ae76acb@mail.gmail.com>
> Joseph Cole <coljo582@student.otago.ac.nz> writes:
>
>> I've been struggling with a few aspects of org babel R:
>>
>> 1) src_R surrounds output with ==.
>>
>> E.g. src_R{1+1} gives =2=
>>
>> I would expect it to just give 2. Because it surrounds the output with
>> equals signs, this means you are unable to use the output in latex
>> equations, general text or tables as it's ugly.
>
> Hi Joseph,
>
> If you use ':results raw', then the results will be inserted without the
> surrounding '='. You will need to pull the latest git head as I just
> fixed a bug regarding that. So you could use
>
> src_R[:results raw]{1+1}
>
> but to make it less clumsy you could configure
> org-babel-default-inline-header-args, e.g.
>
> (setq org-babel-default-inline-header-args
> (org-babel-merge-params org-babel-default-inline-header-args
> '((:results . "raw"))))
>
> after which
>
> \begin{equation}
> 1 + src_R{1+1} = 3
> \end{equation}
>
> exports to latex as
>
> \begin{equation}
> 1 + 2 = 3
> \end{equation}
>
> As for the default behaviour, the == declares that the contents should
> be formatted fixed-width on export. Normally in latex export that
> results in \texttt{}, but I see that inside a begin_equation the ==
> remain. I wonder whether that could be argued to be an org-mode latex
> exporter bug?
Thanks for the help, I'm pulling down the head to test.
It certainly would make more sense to embed raw automatically within
equations.
>
>>
>> Where should I start looking to fix this? I'm a lisp novice but happy
>> to learn.
>
> org-babel-exp.el
Thanks. The code makes sense.
>> 2) Width/Height exports for R graphics output. Do they work?
>>
>> I've tried a lot of combinations of :width and :height as exports, and
>> they don't seem to work at all. I've tried small numbers (1-10), large
>> numbers (100-2000) and numbers prefixed by "cm" with no luck.
>
> Hmm, I'm not seeing a problem here. It works for me with both png and
> pdf output. E.g.
>
> #+begin_src R :file z.pdf :width 20 :height 40 :exports both
> plot(1:10)
> #+end_src
> What image format (i.e. R graphics device) are you using? Can you post
> an example block that is not working? The values for :width and :height
> will be passed straight on to the graphics device, so their meaning
> depends on which graphics device is being used in R.
I'm trying the code you posted with the latest org-mode from ubuntu
and getting nothing in my results if I use png. If I use pdf, I get a
really tiny chart which is incomprehensible. Width and height seem to
work randomly, as using 20:40 work with pdf (although tiny), but
100,100 do not work at all.
It only works correctly if I use the #+attr_latex: width=Xcm and omit
the width and height.
I'm using ubuntu jaunty fully up to date, org mode from the website
(6.34c), R 2.92, and the stock standard latex install for ubuntu.
>
>>
>> I know I can use #+attr_latex: width=15cm.
>>
>> 3) R-graphics quality
>>
>> I can't seem to find any examples of how to set the R graphics output
>> quality, and nothing I try seems to alter the result (using :quality).
>
> I'm not sure what you mean by "R graphics output quality". The section
> "Graphical output" in
>
> http://orgmode.org/worg/org-contrib/babel/languages/org-babel-doc-R.php
>
> describes how to pass arguments to the R graphics devices. In addition
> to the ones that org-babel knows about like :width, you can pass
> arbitrary extra arguments to the R device using :R-dev-args.
>
>>
>> Are there any publication quality r-graphics examples I could take a
>> look at, as I've been unable to find any on google.
>
> You mean using org-babel or just using R?
Using babel. For some reason my R graphics embedded within my pdf's
don't seem to be as "nice" as viewing them from within R, i.e.
slightly fuzzy edges. It's like the antialiasing has failed or
something. The text labels on the axes are definitely not up to latex
standard.
Best regards,
Joe
next prev parent reply other threads:[~2010-03-21 9:18 UTC|newest]
Thread overview: 6+ messages / expand[flat|nested] mbox.gz Atom feed top
2010-03-19 8:01 Org babel R Help Joseph Cole
2010-03-19 14:30 ` Dan Davison
[not found] ` <5084fc611003210151x41850afcg36b275679ae76acb@mail.gmail.com>
2010-03-21 9:18 ` Joseph Cole [this message]
2010-03-21 9:53 ` Graham Smith
2010-03-21 14:19 ` Dan Davison
2010-03-21 17:45 ` Graham Smith
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