Play with this; learn things; ask questions (with apologies to Scott Bakula):

#! perl -slw
use strict;
use Data::Dump qw[ pp ];

## Input to separate arrays
my( @xs, @ys );
( $xs[ @xs ], $ys[ @ys ] ) = split while <DATA>;

## cross xs with ys and get pop count of pairings
my %freq;
for my $x ( @xs ) {
    ++$freq{ sprintf "%.2f %.2f", $x, $_ } for @ys;
}
#pp \%freq;

## most plotters require input as vectors, so split them out
my( @rx, @ry, @rz );
( $rx[ @rx ], $ry[ @ry ], $rz[ @rz ] ) = ( split(), $freq{ $_ } ) for 
+keys %freq;

## print them as line vectors
print "@rx";
print "@ry";
print "@rz";

__DATA__
1 2
3 4
5 6
7 8
9 0
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Output:

C:\test>1163636
9.00 3.00 9.00 5.00 7.00 9.00 1.00 7.00 3.00 1.00 1.00 9.00 3.00 3.00 
+5.00 9.00 3.00 1.00 5.00 7.00 7.00 5.00 7.00 1.00 5.00
6.00 8.00 0.00 8.00 2.00 8.00 2.00 6.00 2.00 8.00 4.00 2.00 4.00 6.00 
+0.00 4.00 0.00 6.00 4.00 8.00 4.00 2.00 0.00 0.00 6.00
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
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