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The formula you have written is for when you taking angle $\omega t$ from horizontal $x$-axis but in your case, the point is starting from the y-axis thus it's necessary to take the angle $\omega t$ from the positive y-axis. This will turn your formula to $$y=r\cos(\omega t)$$ $$x=r\sin(\omega t)$$ Now you can proceed from here. :)