The Harmony line operates most conventionally in Classical Mode. The notes in your piece (with the exception of sixteenth notes) will be altered to fit the current chord, which by default is C Major.

Local harmonic gestures (smooth curves in the Harmony Line) will create standard progressions from the chord of the tonic (I) to the chord of the dominant (V or vii) at the junction of the green and blue shaded background regions. The music will then resolve back to the tonic by the end of the blue-shaded region.

Modulating gestures (spikes in the Harmony Line) will create a chord progression which modulates, again via standard chord progressions, to a new key determined by the height or depth of the spike. The precise tonal path of these progressions is a function of the width of the spike or duration of the yellow-shaded area.