There must be loss of accuracy: coordinates in PDF are recorded to
finite accuracy (for pdf(), something like 0.01" as I recall). In
addition, the R plot engine assumes finite accuracy, a minimum width for
lines .... And as people are pointing out, so do PDF viewers.
Do not expect to zoom into a plot (PDF or otherwise): if you want a
large plot, plot it large in the first place.
On 17/04/2012 13:58, Marc Schwartz wrote:
On Apr 17, 2012, at 7:08 AM, Unger, Kristian, Dr. wrote:
Hi there
is it possible that pdfs generated using the pdf() function with default
settings leads to loss of information? I was plotting copy number changes from
Agilent 180k data in form of rectangles (rect()) while each rectangle
represents one region of copy number change. When plotting into a pdf I noticed
that some very small rectangles do not appear (even after extensive zooming) in
the pdf using the pdf() function. But they do when writing the screen output
into a pdf using the GUI. Does anyone have some advice on this how I can plot
pdfs without losing information?
Best wishes
Kristian
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
Which is already 3 versions old: see what the posting guide has to say
about that ....
locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] CGHregions_1.12.0 CGHcall_2.14.0 CGHbase_1.12.0 marray_1.32.0
[5] limma_3.10.3 Biobase_2.14.0 DNAcopy_1.28.0 impute_1.28.0
loaded via a namespace (and not attached):
[1] tools_2.14.0
If you can provide some reproducible code (small example that yields the
problem), that would help. However, you may be experiencing a problem in your
PDF viewer (Preview?) due to anti-aliasing, which is noted here:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-are-there-unwanted-borders
Regards,
Marc Schwartz
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--
Brian D. Ripley, rip...@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
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