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I should have explained more.
point = [wx, wy, wz]
if not self.plotdata or point != self.plotdata[-1]:
self.plotdata.append(point)
This adds a plot point. We would need to change it to also add color.

point = [wx, wy, wz,color]
or maybe better:
self.plotdata.append([point, color])

then later in the file:
#GL.glColor3f(1.0, 0.5, 0.5)

GL.glBegin(GL.GL_LINE_STRIP)
for p,c in self.plotdata:
GL.glColor3f(*c)
GL.glVertex3f(*p)
GL.glEnd()

a few other initialization and clearing details to follow up. but that might work.

Another update.  It seemed that I didn't have the Mesa tied to ground properly.  It is now tied to earth ground (I also tied the shielding into earth ground). The jittering all went away and now the 'hm2_7i96s.0.periodm.00.duty_cycle' is sitting at 0 even when the EDM is running.  Anyone have any ideas? 

Is 'hm2_7i96s.0.periodm.00.duty_cycle' the correct pin?