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When getting events from (read-event) it's possible to access only mouse events using (mouse-movement-p event).
Inspecting the events I've found I can get the Y pixel location using (cdr (nth 2 (nth 1 event)) however this seems overly cryptic.
What is a good way to access data in mouse motion events?
There is a list of functions with the posn prefix to extract that information and more from mouse events. One caveat is that many of them require a start/end event:
(let ((e (read-event)))
(when (mouse-event-p e)
(let ((x-y (posn-x-y (event-start e))))
(message "Mouse event at: %d|%d" (car x-y) (cdr x-y)))))
C-h f posn-x-y.