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There is currently no tool which has the capability to add the lines in a user friendly way. I created a simple function, acting in a very similar way to classic boxplot(), implementing the automatic line creation.

Instead of calling

boxplot(data, groups, labels)

you simply call

boxplotdifferences(data, groups, diffs, labels)

where diffs is a double matrix containing info about the difference lines. Each row represents a single difference. First column is the position of the group A, second column the position of group B and third column is the degree of significance (1 - *’, 2 - ‘**’, 3 - ‘***’). For example, the image on this page is described as

diffs = [1 2 2; 1 3 1; 1 4 3];

Check the git repository below: