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Is it possible to run javascript on plugin deactivated and if yes then, how should I achieve that. I have developing one plugin in which two new tables are created in wp database and on deactivation I want to confirm from users if he/she wants to delete those table before deactivating.

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This is really a javascript question, but there is nothing preventing you from doing a regular confirm with AJAX.

For example: http://stackoverflow.com/questions/8680491/javascript-confirm-with-php-function-afterward

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