Hi Ian,
Not 100% sure on this, but I've recently been wrestling with producing
plots in R and I think I know the answer to your question. As far as I
could tell, all the parameters for graphics are stored using par().
There is a parameter $bg, which for me is set to transparent, but
I'll bet
What is d1? The plot function itself is generic and does not
necessarily do anything. It might be that the d1 object is of a
particular class and the plot method for that class changes the
background, point color, etc. You could try
par(bg = transparent)
but it's possible that the plot
