Publication quality graphics in R

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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

How do i remove myself from this list?

Quoting Nicholas Lewin-Koh <nikko at hailmail.net>:

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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~