You can include jQuery calls anywhere in your php page. The code needs to be inside <script> tags and be called by jQuery function.
Below is a simple example of a button that will disappear after you click on it.
$html = '<button id="clickme">Click on Me</button><div class="showme" style="display:none">Some text</div>;
echo $html;
And the jQuery script below makes the text appear and the button disappear after it has been clicked.
$html = '<script>
jQuery(document).ready(function($) {
$("#clickme").click(function(){
$(".showme").show();
$("#clickme").hide();
});
});
</script>';
echo $html;