This could be written like this:

<?php if (showmessage($msg)): ?>
    <script>
        $(document).ready(function (){
            jqxAlert.alert('Alert Message');
        });
    </script> 
<?php endif; ?>

Or like this:

<?php if (showmessage($msg)) { ?>
    <script>
        $(document).ready(function (){
            jqxAlert.alert('Alert Message');
        });
    </script> 
<?php } ?>

Or like this:

<?php 

    if (showmessage($msg)) { 
        echo
        '
            <script>
                $(document).ready(function (){
                    jqxAlert.alert(\'Alert Message\');
                });
            </script> 
        ';
    } 

?>

Or even this (probably not the best idea though):

<?= (showmessage($msg)) ? '<script>$(document).ready(function (){jqxAlert.alert(\'Alert Message\');});</script>' : ""; ?>

Alternatively, if you mean you would like to put the error message in that alertbox

<?php 

    if (showmessage($msg)) { 
        echo
        '
            <script>
                $(document).ready(function (){
                    jqxAlert.alert('.showmessage($msg).');
                });
            </script> 
        ';
    } 

?>

and again in the first style

<?php if (showmessage($msg)): ?>
    <script>
        $(document).ready(function (){
            jqxAlert.alert(<?= showmessage($msg) ?>);
        });
    </script> 
<?php endif; ?>