To represent or express in the form of a diagram; to create a diagrammatic representation of something.
From diagram plus -matize (from -matic plus -ize), creating a verb meaning 'to render diagrammatic.' This is a constructed term combining productive English suffixes.
The -ize suffix means 'to make or become'—'diagrammatize' theoretically means 'to make diagrammatic,' but it's so rare that most English speakers would just say 'diagram it' instead. This shows how English has multiple ways to say the same thing at different formality levels.
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