Atomic orbitals: 3s electron density
The "surface" of the orbital represents points for which the electron density for that orbital is the same  an isosurface. By choosing different values of electron density, denoted by the bar moving up and down on the line plot or by the moving plane on the surface plot, then the size of the 3d plot changes. This plot also shows that the magnitude of the electron density for the inner lobes is high so that if we choose a high threshold value (when the bar is high), then we only see one or more of the inner lobes in the threedimensional plot. Only by moving the bar down sufficiently far does the main outer lobe become visible.
As the wave function is directionless, so is its square. All values are of necessity not negative since the square of any real number cannot be less than zero.
