Here is a simple function to rotate a non-square image 90 degrees clockwise.

<?php
function rotateImage($imageResource)
{
    $width = imagesx($imageResource);
    $height = imagesy($imageResource);
    $side = $width > $height ? $width : $height;
    $squareImage = imagecreatetruecolor($side, $side);
    imagecopy($squareImage,$imageResource,0,0,0,0,$width,$height);
    $squareImage = imagerotate($squareImage,270,0,-1);
    $imageResource = imagecreatetruecolor($height, $width);
    $x = $height > $width ? 0 : $side - $height;
    imagecopy($imageResource,$squareImage,0,0,$x,0,$height,$width);
    return $imageResource;
}
?>