[R] loss of information in pdf plots

[Marc Schwartz]

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)
> 
> 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