Nona, that's interesting. Here, it's much more common to put your title, then a comma, and then your department. I'm Manager, Corporate Communications. My boss's boss is Vice President, Communications. Would it be more natural to you that I be Corporate Communications Manager?
Deputy Director says clearly to me that you report to the director as his second in command - although (now that I think about it) it could be that the director is the head of everything, and she has a deputy director for R&D, another deputy director for operations, another deputy director for sales, etc. That's how it works in a lot of government positions, though some get quite silly - assistant deputy director for the under secretary of X.
In any case, do NOT break up deputy and director with the R&D between it.