Very basic question but I am struggling to get my head around it as it seems to me that I am trying to plot 4 variables ...
Is it possible to visualize the variation of a quantity, given that it is a (unknown) function of 3 variables, on one plot? [Essentially the data I have is the coordinates of an ion in 3d space and its energy at that point].
The answer is that it is indeed possible. The following link shows some ways of visualization for a Cosmic Ray (CR) problem in astronomy:
CR pressure with AVS
AVS = "Advanced Visualization System" (: let Google be your friend). I don't know if meanwhile there are cheap (i.e. non-commercial) alternatives for the latter.
One method is to plot the energy of the ions as colored dots. Example: