"I want to have one colour per unique peptide, [...] I would like peptides of a similar frequency to be the same colour"

Isn't that contradictory?

Yes!! I should have said I want one colour per peptide frequency, sorry

The keys of

  %frequencyColors = reverse %bindersBla

are the different frequencies.

scalar keys will give you the number.

Now you are free to set the values to colors.

Please show some effort and try to hack it by yourself now.

update

To late. ...

Cheers Rolf
_{(addicted to the Perl Programming Language and ☆☆☆☆ :)
Je suis Charlie!}

So, does this help?

#!/usr/bin/perl                                                       
+            
use strict;
use warnings;

use Color::Spectrum qw/generate/;
use List::MoreUtils qw/uniq/;
use Data::Dump qw/pp/;

my %peptides = (
    HISCLTFGR => 16,
    MQLFHLCLI => 8,
    WGMDIDPYK => 4,
    YVNVNMGLK => 3,
    AYRPPNAPI => 2,
    ELMNLATWV => 2,
    EYLVSFGVW => 1,
    FFPSIRDLL => 1,
    FLPSDFFPS => 1,
    IISCSCPTV => 1
    );

my @unique_indices = uniq values %peptides;
my $num_colours = scalar @unique_indices;
my @colours = generate($num_colours, '#FF0000', '#0060BF');
my %values_to_colours;
$values_to_colours{$unique_indices[$_]} = $colours[$_] for 0..$#colour
+s;


pp %values_to_colours;
[download]

Yes!! Sorry, I can see the error of my logic. I would in fact like one colour per peptide frequency