Though R plots sent to a PDF can be rescaled at will in an illustration or page layout software, scientific journals often insist that the plots provided have specific dimension
An option equally good or better than pdf is tiff. All journals I have come across like tiff.
tiff(filename="name.tiff", width=5, height=5, units="in",
pointsize=8, compression="lzw", bg="white", res=600,
restoreConsole=TRUE)
qplot(data=iris, x=Petal.Width, y=Petal.Length, colour=Species)
dev.off()
If you are on linux, drop restoreConsole=TRUE
, seems only windows likes that.