A three-dimensional delayed detached eddy simulation (DDES) has been carried out to investigate the tonal flow dynamics of an over-expanded transonic subscale planar nozzle at low nozzle pressure ratio (NPR = 2). Here we compare modal decomposition techniques; namely, proper orthogonal decomposition (POD), which ranks modes based on energy, and dynamic mode decomposition (DMD) which ranks modes based on growth rates (and also their corresponding Ritz eigenfrequencies), in visualising aero-acoustic mechanisms in the over-expanded nozzle flow. We find that both are able to educe the dominant tonal flow dynamics, particularly with respect to the transonic resonance tone, but also their ability to visualise fluctuating signatures existing in the separation bubble, which are believed to be responsible for supporting upstream propagating waves for closure of the transonic resonance and/or screech loops.