This phrase implies someone's unique way or approach often admired or recognized by others. His humor has a way of easing tense situations.
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Not Literal
The 'way' of doing something is often figurative, referring to one's approach rather than a physical path. She has a way of organizing her thoughts that's quite effective.
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Admirable Skill
Often used to compliment someone's skill or technique in doing something well. He has a way of negotiating that always seems to work.