If all you want to know is the contrast, you don't need to generate a graph. Just use the distance formula to calculate the separation of each pair of points. That gives you a single number for each pair, and a larger number indicates greater contrast.

Given points A (Xa, Ya, Za) and B (Xb, Yb, Zb), plug the values into this:

sqrt( (Xa-Xb)2 + (Ya-Yb)2 + (Za-Zb)2 )