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The lighter shades correspond to the larger entries of the matrix. In your example the black square are in positions (0, 1) and (2, 1), where the entries are -1, and the white square is in position (0, 0), where the entry is 3, which is the largest entry in the matrix. Typing

sage: M = matrix([[3,-1,1],[2,0,1],[1,-1,2]])
sage: M.plot?

will give more information.