The top line (light blue) represents the amplitude of the pendulum. The higher the line, the wider the amplitude. It's actually a measurement of how long the pendulum blocks the optical sensor each time it passes through center. The duration of this time is shown on the right side of the graph (about .023 seconds). The wider it swings, the faster it swings through the center.
The bottom line (brick red) is the rate of the pendulum, near 1.25000 seconds per beat. The lower the line, the slower the clock is.
The reason for the interaction of these two parameters is "circular error". In a pendulum clock, the pendulum swings in a circular arc because the pivot point is fixed. (If you want to get picky, there is debate about whether or not the pivot point moves up and down as the suspension spring flexes. But generally speaking, a pendulum bob swings in a nearly circular arc.)
But a circular arc is not isochronous. This means that, when the arc is wider, the pendulum takes longer to swing from one side to the other. Christiaan Huygens recognized this problem with amplitude in the 17th century, and determined that a pendulum needed to swing in a "cycloidal" arc to be isochronous. Many people have tried to make pendulum clocks that swing in a cycloidal arc, but it ain't easy. Instead, precision clocks are made to swing with small amplitudes. With a small amplitude, the deviation of a circular arc from a cycloidal arc is small, and clock rate is less effected by inevitable changes in amplitude. But as the amplitude increases, the effect on timekeeping increases.