Each column is a single pony’s cutie mark, and the columns have been arranged alphabetically according to whose cutie mark it is. Each row is a different number of “shifts” from the normal palette.
If you would have done it differently, I’d be interested in seeing what you come up with; I’m sure there are tons of ways! (For example, striping each symbol within a mark with all three colors of Rainbow’s lightning bolt instead of making each one a different color.)
I do not intend this chart as a shipping thing, but I suppose I won’t stop anyone from using it as such.