I could be wrong, but it looks like you are using coordinate pairs. The following sorts coordinate pairs with y in descending order and x in ascending (since you didn't specify x to be descending as well):

use strict;
use warnings;

my ($x, $y, $ref);
for (0..20) { # Randomize some data points for testing
    $x = int rand 100;
    $y = int rand 100;
    $ref->[$_] = [$x,$y];
}
for (sort {$b->[1] <=> $a->[1] or $a->[0] <=> $b->[0]} @$ref) {
    print $_->[0] . ',' . $_->[1] . "\n";   
}
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