[R] Using graphics straight from R into published articles

[Rainer M Krug]

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On 29/03/11 19:52, Philipp Pagel wrote:
> On Tue, Mar 29, 2011 at 09:31:18AM -0700, blanco wrote:
>> I was just wondering if people use graphics from R straight into articles or
>> are they always edited  in some way; fonts, headers, axis, color etc?  Using
>> photoshop or some other programs?
>>
>> I would like to think it is possible, better and more profession to do it
>> all in R.

Absolutely. You can get one paper = one file (if you want to, including
your data - but usually that one is separate) when you use e.g. sweave
or org-mode babel (http://orgmode.org/,
http://orgmode.org/worg/org-contrib/babel/) - all graphs are generated
when you compile your document. I use org-mode.

>> I tried google and the search option but found nothing on the topic.  
>>
>> What are the experiences for all the professionals out there that use R?
>> Are there any articles on this specific subject?
> 
> I'm not aware of any articles on the topic but I can share what I do:
> 
> 95% of the time I tweak various graphics parameters in R and see no
> necessity for postprocessing in other applications.

Up to now, even 100%

> 
> In about 5% I do some manual editing for a "camera ready" figure.
> These are usually the result of exotic request from referees. But
> under no circumstances would I use Photoshop or any other pixel
> graphics software for this. My R graphics are always created as eps or
> pdf vector graphics and any editing is done with a proper vector
> graphics software (Illustrator or Inkscape).

Absolutely vector - no jpeg, png, ... although it takes sometimes some
convincing of co-authors...

> 
> I share your feeling that it is better to do as much as possible in R
> because it means that I won't have to do it again if I need to produce
> another revision of the figure - all it takes is anoother run of my
> script. And I can re-use good solutions in the future. Any manual
> touch-ups have to be done manually every single time => not my idea of
> efficiency.

Absolutely - reproducible research. And if you have several graphs, they
all share the same layout, font, fontsize, margins, ...

I rather spend an hour fiddling on my graphs in R (and sometimes
swearing about the layout of multiple graphs in one figure) then spend
half an hour "painting" my graphs.

Cheers,

Rainer

> 
> cu
> 	Philipp
> 


- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

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