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inner sep=0,outer sep=0を使うと良さそう

tex.stackexchange.com/question

\node (O) [inner sep=0,outer sep=0]{$\otimes$};
\node (X) [right of=O]{$x$};
\node (Y) [above of=O]{$y$};
\draw[->] (O) -- (X);
\draw[->] (O) -- (Y);

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