As far as PHP is concerned (or really, a web server in general), an HTML page is nothing more complicated than a big string.
All the fancy work you can do with language like PHP - reading from databases and web services and all that - the ultimate end goal is the exact same basic principle: generate a string of HTML*.
Your big HTML string doesn't become anything more special than that until it's loaded by a web browser. Once a browser loads the page, then all the other magic happens - layout, box model stuff, DOM generation, and many other things, including JavaScript execution.
So, you don't "call JavaScript from PHP", you "include a JavaScript function call in your output".
There are many ways to do this, but here are a couple.
Using just PHP:
echo '<script type="text/javascript">',
'jsfunction();',
'</script>'
;
Escaping from php mode to direct output mode:
<?php
// some php stuff
?>
<script type="text/javascript">
jsFunction();
</script>