Can you take the R train by Atlantic to get to Queens Plaza?

Are you asking if you can take the R train from the Atlantic Avenue-Pacific Street station to the Queens Plaza station? If so, then, yes, you can take the R train from Atlantic Avenue-Pacific Street to Queens Plaza, except from 11 PM to 5:30 AM, when there's no service.

From 11 PM to 5:30 AM, I guess you could take the N train (on the same line, the N-R-Q-W, the yellow line) from Atlantic Avenue-Pacific Street to Queensboro Plaza (which is a different station a few blocks northwest of the Queens Plaza station) and walk the rest of the way.