Exclude value if under a certain percentage

I think what you need is to filter your dataset before calling chartjs to create the chart. Is there any reason not to do that?

$sumofvars=array_sum($output);
$above_percent=0.1;

    foreach($output as $compound => $sum){

$percentage_to_eliminate=($sum/$sumofvars)*100;

if ($percentage_to_eliminate>$above_percent)
{

 echo "{category: '".$compound."', value: ".$sum."}, ";

}

    }      
    ?>      
];