They asked people in different places a lot of questions about the values important to them. They then used math to decompose all those answers into two themes ("tradition" vs "secular" and "survival"/"responsibility" vs "self-expression" and averaged by country and put a dot for each country on the chart. The colored bubbles aren't from math though, they're just the writers' drawing lines around countries with historical affinities for each other, and showing how closely their people's values are today.