Fix plot_peripheral_frequency

@Leo-Yan I made a few changes to plot_peripheral_frequency/df_peripheral_clock_effective_rate, let me know if everything still works for you.

Wrt to the trace for the documentation plot, it seems that juno:uartclk does not have any event for clk_set_rate, so I switched to aplclk to get a more interesting plot.

The plot can be quickly viewed (with that PR) using:

lisa-plot doc/traces/trace_peripheral_clk.dat --plot frequency:peripheral-frequency interactive -X clk_name aplclk