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I assume, that you understand, that changing the PWM frequency mainly involves timer programming and also scaling of output values. You can basically make the PWM frequency (respectively period) depend on a variable value in your application. If you manage it, then it's easy to use e.g. an analog input to control it, and connect a variable resistor or potentiometer as a control.
The said additional calculations needed in set-point scaling may however reduce the performance of your PWM. A very basic method to tune the PWM frequency would be in using an external RC oscillator for the processor and tune it by a resistor. The processor will be rather slow in this case, and all processor frequency based timing and baud rates will be varied as well.