Yellow dots for atom centres

[RachelAlcraft]

Add, optionally by a toggle, yellow does to show the input points. Optionally also project the atoms to the plane in a different colour.

[RachelAlcraft]

Overlaying 2 plots in plotly - try this first: https://stackoverflow.com/questions/37927746/how-to-plot-two-plots-in-the-same-figure-in-plotly-js