Let me play with this:
A. Duplicate your sphere
B. Duplicate your row and place it a bit down
C. And move it a bit to one side, to the left on this example.
D Repeat several times.
This could be one "isometric" style (It is not really isometric) but you do not have any perspective at all.
F. So you could now scale the second row and keep scaling the next ones.
G. This also works.
H. But now, if you move them to the left as the other example, it looks distorted.
I. So, you now need to scale incrementally also on each row
J. But now it looks like the graph is rolled, so
K. Compensate a bit rolling to the right.
L. You can do the same modifications to the Z axis. I will just duplicate the "isometric" version.
But you will notice now that the layer below, should not "glow" because it has a layer of spheres above...
If you are ok until this point, keep doing it in 2D software. But if you want more realism... Switch to 3D
(This image was way faster than the 2D versions)