How do I process IQ data received from a signal analyzer
If you're looking for the phase progression I would recommend not using atan() in MATLAB to extract the phase angle.  Use the built-in function angle() to extract the phase from the complex samples properly accounting for the quadrant of the complex plane in which each sample appears.  This resulting phase can then be unwrapped.

unwrappedPhaseRad = unwrap(angle(inputComplexSamples));

where unwrappedPhaseRad is the unwrapped phase in radians and inputComplexSamples is a vector (1 dimensional array) of your complex input data samples.