ddply can be very slow. Strongly recommended to get your data into the form you want in something map-reduce-y _then_ throw it into R for analysis and graphing.
I have been using R daily for 7-8 years now and have only occasionally turned to somethig like data.table for performance reasons. "Big data" receives waaay more attention and hype than there are actual human beings working on data of that scale. I can assure you that for the vast majority of R users world wide plyr is plenty fast enough for their needs.