Monthly mean atmospheric CO2 in PPM at Mauna Loa, Hawaii (source: NOAA/ESRL).
If you tell Flot that an axis represents time, the data will be interpreted as timestamps and the ticks adjusted and formatted accordingly.
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The timestamps must be specified as Javascript timestamps, as milliseconds since January 1, 1970 00:00. This is like Unix timestamps, but in milliseconds instead of seconds (remember to multiply with 1000!).
As an extra caveat, the timestamps are interpreted according to UTC to avoid having the graph shift with each visitor's local time zone. So you might have to add your local time zone offset to the timestamps or simply pretend that the data was produced in UTC instead of your local time zone.