[R-sig-eco] Publication quality graphics in R

[Nicholas Lewin-Koh]

Hi,
following this thread I have seen several misunderstandings that I think 
should be cleared up. Firstly, we should be careful what is meant by 
"publication quality", on interpretation is for a particular journal,
a good resolution graphic in the format they require. In general, the
meaning refers to the quality and portability of the graphic for
publishing
in different media while retaining as much of the original detail as
possible.
Some journals require submission in MSworst, for importing graphics 
into a word document, wmf  is microsucks vector format, and is
probably the most suitable for most statistical graphics. For images
a bitmap format like png or tiff is  most suitable. I would avoid jpeg,
as the main purpose of jpeg is compression. If you need to edit
a graphic outside R, wmf, and svg will allow you to ungroup the graphics
components and edit them individually in most good drawing programs.
Personally
I have had good experiences with svg and inkscape. For color graphics
where colour gradients are important, I would recommend exporting
and viewing the graphics in a program with good colour management. R is
not tied to a colour management system and it is trial and error to
get colours printed correctly. There has been some discussion of
incorporating
little cms, but that is probably a good "google summer of code" project. 

In regards to the post below, as of R 2.7, alpha blending is supported
on most devices if R was compiled with cairo. This is the case
for the windows distribution, and the default for configure when
compiling
from source on linux.

<\begin rant>
As a personal rant I would suggest that most journals don't publish
publication quality statistical graphics, as most scientists don't
produce them.
Biological journals are full of crammed bar graphs with antennae on top,
with
six different fills, that as far as I can tell contain very little
information.
All the work done on how to represent information with grammar and
aesthetics
goes out the window in journal publications.
<\end rant> 

My 2c. So flame me.

Nicholas

> ------------------------------
> 
> Message: 2
> Date: Sun, 01 Jun 2008 10:47:49 -0400
> From: Phil Novack-Gottshall <pnovackg at westga.edu>
> Subject: Re: [R-sig-eco] Publication quality graphics in R
> To: r-sig-ecology at r-project.org
> Message-ID: <200806011448.m51EmWOO008811 at hypatia.math.ethz.ch>
> Content-Type: text/plain; charset="iso-8859-1"; format=flowed
> 
> [Apologies if this is a duplicate; I seem to be having e-mail problems.]
> 
> I've also had trouble dealing with formatting 
> issues from R to a format acceptable for 
> journals.  But I found a really useful 
> recommendation from Cadmus, the art folks for 
> PNAS.  Here's a useful site: 
> http://cpc.cadmus.com/da/tutorials.jsp and 
> http://art.cadmus.com/da/instructions/ps80_win.jsp 
> They're not specific to R, but there's some good general advice.
> 
> I, too, tend to save images as a .pdf 
> (specificying final size and resolution), and 
> then convert to TIF or EPS using the following (also advised from
> Cadmus):
> 
> For EPS:
> Once you have a PDF file, you can open it with 
> the ?full? version of Acrobat and then do a ?Save 
> as EPS? ? or ? you can open your PDF with Illustrator and then ?Save as
> EPS.?
> 
> For TIF:
> Open the PDF file from within Photoshop. This 
> will allow you to determine resolution 
> (typically, 600 DPI is ideal for most figures). 
> While in Photoshop, go to the menu and click 
> "Layer>Flatten Image", crop (trim) excess white 
> space around the figure, scale it to the correct 
> size, and then "Save As?" a TIF file using LZW (not JPEG or ZIP)
> compression.
> 
> This usually works for the journals I've dealt 
> with.  And a benefit of saving directly as PDF is 
> you can use the alpha functionality in 
> color.palette() to set transparency, which is 
> really useful when having overlaying colors.  (To 
> my knowledge, alpha is not allowed when plotting in the R window.)
> 
> Phil
> 
> 
> > > I'd like to hear from the list, how folks specify and export presentation
> > > quality and publication quality graphics with R.  I've had problems
> > > when exporting graphics using the copy-to-clipboard option (both bitmap
> > > and metafile)
> > > and also when saving them as jpgs.  They almost always seem to look a
> > > little funny
> > > (e.g. pixelation, symbols coming out distorted etc.).  The only option
> > > that I've had
> > > much success with is saving them as pdf's, but that format is less than
> > > ideal when trying
> > > to incorporate a graphic into another document (e.g. Word or Powerpoint),
> > > and is often
> > > not the format requested by journals.
> > >
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>    Phil 
> Novack-Gottshall 
> pnovackg at westga.edu
> 
>    Assistant Professor
>    Department of Geosciences
>    University of West Georgia
>    Carrollton, GA 30118-3100
>    Phone: 678-839-4061
>    Fax: 678-839-4071
>    http://www.westga.edu/~pnovackg
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~