I am using 3D scatter command using the following syntax: scatter3(X,Y,Z,S). The arguments x1 and y1 define the arguments for the first plot and x1 and y2 for the second. [ax, h1, h2] = plotyy (…) Plot two sets of data with independent y-axes and a common x-axis. By default the arguments are evaluated with feval (@plot, x, y). The marker size is variable in my case where S is a vector.

But the marker size is not in scale with the plot axes.