position

The pm3d colored surface can be drawn at the true z position of the surface or projected onto the base plane or the top plane. This is controlled by the at option with a string of up to 6 combinations of b, t and s. For instance, at b plots at the bottom only, at st plots first at the surface and then on the top plane, while at bstbst is unlikely to be useful.

Colored quadrangles are plotted one after another. That means later quadrangles can occlude or overlap the previous ones. You may try to switch between scansforward and scansbackward to force the first scan of the data to be plotted first or last. The default is scansautomatic where gnuplot makes a guess about scans order. The depthorder option completely reorders the quadrangles by sorting on the distance from the viewpoint. This allow to visualize even complicated surfaces; see pm3d depthorder for more details.