It is fairly straightforward to set the margins of a graph in R by calling the par() function with the mar (for margin!) argument. For example, par(mar=c(5.1,4.1,4.1,2.1) sets the bottom, left, top and right margins respectively of the plot region in number of lines of text. Another way is by specifying the margins in inches

Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).