My guess is that you only show a few plots to your "organisation"
among all those you produce. One solution would then be to fix the
issue manually: open up the plot in a vector graphics editor
(Inkscape, Adobe Illustrator) and just move the tick marks inside. I
should take you a minute per plot at most and the development version
of Inkscape deals with PDFs or SVGs produced by R very well.
I know there are strong opinions about that and some people firmly
believe that touching the plot after it is produced is against the
principle of reproducible research. I personally think that, when it
is for some cosmetic fixes such as this one, that, in addition, might
be "wrong" hence not encouraged by the plotting package (cf Hadley
argument above), this is perfectly acceptable. Now, you'll have to
make your own opinion.
JiHO
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http://jo.irisson.free.fr/