R help - May 2008 - Preparing high quality figures with tiff as end result

Hi all,

I'm currently preparing some figures that will be submitted to PloS One.
In their guidelines they state that they will only accept figures in
tiff or eps format, with the warning that eps figures will be
converted to tiff format ( see
http://www.plosone.org/static/figureGuidelines.action ).

Because of this conversion, I figured I'd generate tiff-format figures
from the beginning.
However, a number of issues cropped up:
1) using

library(Cairo)
CairoTIFF("test.tif")

I get " Sorry, this Cairo was compiled without tiff support.". I tried
finding out how to recompile Cairo, but got lost in a lot of confusing
talk about GTK+, downloaded dll files that I didn't know how to use
etc.

so I turned to plain tiff(), and

2) R started crashing on me.The following code

tiff("test.tif")
plot(rnorm(100))
dev.off()

,crashes R (i.e "R GUI has encountered a problem and needs to
close...") every third time or so.
When it does work, the resulting output is not too pretty.

So I turned to using postscript files. However, Plos One requires that
fonts be embedded into the figure.
embedFonts()  works for this, but the result is that text becomes
low-res bitmaps, and I don't know how to solve this.

So basically my question is: How should I go about generating graphics
that will look as nice as possible given the above constraints?

Many thanks in advance,

Gustaf




-- 
Gustaf Rydevik, M.Sci.
tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
skype:gustaf_rydevik

On Fri, May 23, 2008 at 4:40 PM, Gustaf Rydevik
<gustaf.rydevik at gmail.com> wrote:
> Hi all,
>
> I'm currently preparing some figures that will be submitted to PloS
One.
> In their guidelines they state that they will only accept figures in
> tiff or eps format, with the warning that eps figures will be
> converted to tiff format ( see
> http://www.plosone.org/static/figureGuidelines.action ).
>
> Because of this conversion, I figured I'd generate tiff-format figures
> from the beginning.
> However, a number of issues cropped up:
> 1) using
>
> library(Cairo)
> CairoTIFF("test.tif")
>
> I get " Sorry, this Cairo was compiled without tiff support.". I
tried
> finding out how to recompile Cairo, but got lost in a lot of confusing
> talk about GTK+, downloaded dll files that I didn't know how to use
> etc.
>
> so I turned to plain tiff(), and
>
> 2) R started crashing on me.The following code
>
> tiff("test.tif")
> plot(rnorm(100))
> dev.off()
>
> ,crashes R (i.e "R GUI has encountered a problem and needs to
> close...") every third time or so.
> When it does work, the resulting output is not too pretty.
>
> So I turned to using postscript files. However, Plos One requires that
> fonts be embedded into the figure.
> embedFonts()  works for this, but the result is that text becomes
> low-res bitmaps, and I don't know how to solve this.
>
> So basically my question is: How should I go about generating graphics
> that will look as nice as possible given the above constraints?
>
> Many thanks in advance,
>
> Gustaf
>
>
Oh, and before anyone bites my head of, I forgot the following:

> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] RWinEdt_1.8-0 Cairo_1.4-2
>
, and  I'm using windows XP professional


again, many thanks in advance
/Gustaf


-- 
Gustaf Rydevik, M.Sci.
tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
skype:gustaf_rydevik

Try bitmap(): this produces PostScript and converts with ghostscript.

BTW, everything (including text) in TIFF files *is* 'low-res bitmaps' by
definition, so you cannot avoid this.  Anti-aliasing *may* help, and the 
bitmap() device in R-devel supports it.

On Fri, 23 May 2008, Gustaf Rydevik wrote:
> Hi all,
>
> I'm currently preparing some figures that will be submitted to PloS
One.
> In their guidelines they state that they will only accept figures in
> tiff or eps format, with the warning that eps figures will be
> converted to tiff format ( see
> http://www.plosone.org/static/figureGuidelines.action ).
>
> Because of this conversion, I figured I'd generate tiff-format figures
> from the beginning.
> However, a number of issues cropped up:
> 1) using
>
> library(Cairo)
> CairoTIFF("test.tif")
>
> I get " Sorry, this Cairo was compiled without tiff support.". I
tried
> finding out how to recompile Cairo, but got lost in a lot of confusing
> talk about GTK+, downloaded dll files that I didn't know how to use
> etc.
>
> so I turned to plain tiff(), and
>
> 2) R started crashing on me.The following code
>
> tiff("test.tif")
> plot(rnorm(100))
> dev.off()
>
> ,crashes R (i.e "R GUI has encountered a problem and needs to
> close...") every third time or so.
> When it does work, the resulting output is not too pretty.
Which means what?
> So I turned to using postscript files. However, Plos One requires that
> fonts be embedded into the figure.
> embedFonts()  works for this, but the result is that text becomes
> low-res bitmaps, and I don't know how to solve this.
>
> So basically my question is: How should I go about generating graphics
> that will look as nice as possible given the above constraints?
>
> Many thanks in advance,
>
> Gustaf
>
>
>
>
> -- 
> Gustaf Rydevik, M.Sci.
> tel: +46(0)703 051 451
> address:Essingetorget 40,112 66 Stockholm, SE
> skype:gustaf_rydevik
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595