Lu's suggestion to use PDL is what I would do if you want to run the visualization "live". I would go with moritz's approach if you want to store the visualization as an animation for later playback. Here is a brief example of a 3D visualization of points using PDL adapted from one of the examples from the docs. The nokeeptwiddling3d() function is what allows the changes in position to be plotted while the iteration happens. If you remove that then you can step through each change in position by pressing the "q" key.

#!/usr/bin/perl -w

use strict;
use PDL;

use PDL::Graphics::TriD;


my        $size = 25;
my        $x = (xvals zeroes $size+1,$size+1) / $size;
my        $y = (yvals zeroes $size+1,$size+1) / $size;
my        $z = 0.5 + 0.5 * (sin($x*6.3) * sin($y*6.3)) ** 3;   # Bumps

my        $r = $x;
my        $g = $y;
my        $b = $z;


nokeeptwiddling3d();

for (1..50){

        points3d [$x,$y,$z], [$r,$g,$b];  # Draw several colored dots
        $x+=$y*$z;
}

keeptwiddling3d();
        points3d [$x,$y,$z], [$r,$g,$b];
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