MF changes to plot.assoc.R and plot.assoc.Rd

You are right about this, in that my solution assumes that `ellipse.col` = the default for `col` used in all these functions. It will break if `length(ellipse.col) <2` and does not respect the actual argument passed as `col`.  
The difficulty is that the use of `polygon()` in lines 527-538 is not vectorized, and is done separately for rows and columns, and so requires one of:
* `border` = constant (`gray` as before) in both calls
* `border = ellipse.col[1]` and `border = ellipse.col[2]` in the two calls, as I've done.  This could be amended with a sanity check, in case `length(ellipse.col)<2`. 
* `border = col[i]` and `border=col[i+j]` in the two calls, using the new value of `col` calculated by the end of line 388.

That's more major surgery than I'm prepared to do at this point.