Step 1. Take any "torus knot with n marked points": which for our purposes will mean homeomorphism classes of embeddings from a circle with n marked points, to the torus.
Step 2. Draw it on paper.
In the case of the Coltrane drawing, n = (5 octaves * 13 notes per octive) = 65. The author exhibited 3 non-homeomrphic embeddings of this circle into the torus in the three images below the protractor picture. In particular these are embeddings generated by iterated Dehn twists on the unknot. You can classify them by winding number.
The image right below the aforementioned ones also shows an embedding of a circle with marked points into the torus if we choose to identify the 2 'c's. This time there's only 13 marked points. This suggests the following. To a circle with marked points, one can associate a canonical family, labelled by integers, of circles with marked points as follows: take any covering map of the circle, and declare the union of the fibers over the marked points to be the new marked points. In the case of the music scale analogy, we take the circle with 13 marked points, and this in particular gives a family of circles with 13 * k marked points for any positive integer k, and the musical interpretation is that k is how many octave one chooses to have. In the images mentioned above k = 3 and k = 1 are exhibited.
There's a simple further generalization of all this: we can replace the torus with any topological space. For example, doing this on a higher genus surface or a non-orientable surface would both yield probably interesting-looking diagrams.