R pch plotting in illustator as “q”

Question

Every time I use pch=21 for plotting in R with lattice, my plot plots normally in the R plotting window and in pdf (circles with borders); however when I open a saved pdf versio

Answer 1

?pdf has:

 On some systems the default plotting character ‘pch = 1’ is
 displayed in some PDF viewers incorrectly as a ‘"q"’ character.
 (These seem to be viewers based on the ‘poppler’ PDF rendering
 library).  This may be due to incorrect or incomplete mapping of
 font names to those used by the system.  Adding the following
 lines to ‘~/.fonts.conf’ or ‘/etc/fonts/local.conf’ may circumvent
 this problem.

     
 
   ZapfDingbats
   Dingbats
 
   

 Some further workarounds for problems with symbol fonts on viewers
 using ‘fontconfig’ are given in the ‘Cairo Fonts’ section of the
 help for ‘X11’.

That fontconfig declaration has worked for me in the past (and still does) on my Linux boxes. I suggest you set that or read the other pages indicated in the last of the quoted sentences and see if those fix the problem you are seeing.