Chromosome::Map - Generate GD images of chromosome maps
#!/usr/bin/perl -w # This script produce a chromosomal map with several markers and QTL # interval region. A fake %GC content is added to the chromosome use strict; use Chromosome::Map; my %H = (ADL120 => '25', ADL035 => '5', ADL034 => '4', MCW014 => '110', MCW123 => '89', MCW340 => '70', LEI456 => '132', LEI451 => '130', LEI452 => '130.5', LEI453 => '130.7', LEI454 => '131', LEI455 => '131.4', LEI457 => '132', MCW087 => '50', MCW012 => '12', MCW051 => '51', ADL121 => '26', ADL123 => '27', ADL122 => '26.2', MCW114 => '45', LEI258 => '15', MCW240 => '45.1', MCW247 => '110', LEI556 => '44', MCW614 => '45.2', ADL067 => '5.3', MCW140 => '45.2', LEI056 => '45.6', ); my $map = Chromosome::Map->new (-length => '140', -name => 'GGA5', -height => '500', -units => 'cM', ); my $size = $map->get_map_size; my $units = $map->get_map_units; print "Map size: $size $units\n"; my $mark_track = Chromosome::Map::Track->new (-name => 'Markers', -type => 'marker', ); my $qtl_track = Chromosome::Map::Track->new (-name => 'QTL', -type => 'interval', ); my $GC_track = Chromosome::Map::Track->new (-name => '%GC content', -type => 'feature', -display => 'relative', -render => 'gradient', ); # adding tracks to map $map->add_track($mark_track); $map->add_track($qtl_track); $map->add_track($GC_track); my $nb_track = $map->get_nb_tracks; print "Nb track: $nb_track\n"; # Generating a fake feature relative elements and add them in track # only for illustrative purpose my %GC; for (my $i=0;$i<=5000;$i++) { my $nb = abs ( rand ($size)); my $value = abs ( rand (1)); $GC{$nb} = $value; } foreach my $nb (keys %GC) { my $gc = Chromosome::Map::Feature->new (-loc => $nb, -color => 'indigo', -value => $GC{$nb}, -valuetype => 'relative', ); $GC_track->add_element($gc); } my @Color = qw (blueviolet darkgoldenrod black softblue khaki red blue tomato); foreach my $mark (keys %H) { my $i = abs (int( rand ($#Color) ) ); my $marker = Chromosome::Map::Element->new(-name => $mark, -loc => $H{$mark}, -color => $Color[$i], ); $mark_track->add_element($marker); } # Define QTL element my $qtl1 = Chromosome::Map::Block->new (-name => 'BW', -start => '3', -end => '11', -color => 'darkgoldenrod', ); my $qtl2 = Chromosome::Map::Block->new (-name => 'FAT', -start => '92', -end => '100', -color => 'darkgoldenrod', ); my $qtl3 = Chromosome::Map::Block->new (-name => 'LEAN', -start => '112', -end => '120', -color => 'darkgoldenrod', ); my $qtl4 = Chromosome::Map::Block->new (-name => 'EGG DEV', -start => '95', -end => '115', ); my $qtl5 = Chromosome::Map::Block->new (-name => 'IC', -start => '91', -end => '122', -color => 'blueviolet', ); my $qtl6 = Chromosome::Map::Block->new (-name => 'BORN', -start => '20', -end => '130', ); my $qtl7 = Chromosome::Map::Block->new (-name => 'REPRODUCTION', -start => '20', -end => '130', ); $qtl_track->add_element($qtl1); $qtl_track->add_element($qtl2); $qtl_track->add_element($qtl3); $qtl_track->add_element($qtl4); $qtl_track->add_element($qtl5); $qtl_track->add_element($qtl6); $qtl_track->add_element($qtl7); my $png = $map->png; my $filename_png = "chr_map.png"; open (PNG, ">$filename_png") || die "cannot create file: $filename_png!\n"; binmode PNG; print PNG $png; close PNG;
The Chromosome::Map module can produce chromosomal map image file. It can be used to draw genetic or physical maps. Several tracks (i.e. list of marker) can be add to the chromosomal map: markers track and QTL interval region track (see synopsis). A code colors list is available at http://chicken.genouest.org/documentations/chromosomemap/#colors
This section describes the class and object methods for the Chromosome::Map module.
First, you will begin by creating a new Chromosome::Map object:
my $map = Chromosome::Map->new ( ... options ... );
The new() method creates a new panel object. The options are a set of tag/value pairs as follows:
Option Value Default ------ ----- ------- -name title name of the chromosomal map none -start location start of the map 0 -length size of the map (i.e location end) none -units unit of the map (i.e cM or MB, only for display) none -height size of the resulting image (pixel) none -pad_left left margin 20 -pad_right right margin 20 -pad_top top margin 20 -pad_bottom bottom margin 40
Public methods description:
add_track: add an existing track to an existing map. return O in case of error
$map->add_track($track)
png: create a PNG image of the map
$name = $map->png
get_map_name: return the title name of the map
$name = $map->get_map_name
get_map_start: return the start location of the map
$map_start = $map->get_map_start
get_map_size: return the end location of the map (i.e. the map size)
$map_size = $map->get_map_size
get_map_units: return the unit of the map (i.e. cM, MB, KB...)
$map_unit = $map->get_map_units
get_nb_tracks: return the number of the tracks in the map
$nb_track = $map->get_nb_tracks
get_list_track: return a list (%Hash) of the tracks in the map
%List = $map->get_list_track
Then, you will create different tracks and add them to the Chromosome::Map object.
my $track = Track->new ( ... options ... ); $map->add_track($track);
The new() method creates a new track object. The options are a set of tag/value pairs as follows:
Option Value Default ------ ----- ------- -name title name of the track none -type this tag will permit you to define the type of the none track with the followin values: 'marker': designed for markers 'interval': designed for QTL interval region, could marker interval or gene location, too 'feature': designed to plot physical features on chromosomes (%GC, nb genes)
if you choose the feature track type, you have to define some other specific options:
Option Value Default ------ ----- ------- -display the tag will permit to define the rendering of the absolute feature track with the following value: 'absolute': if several feature values are present in one pixel interval, the feature values will be added for display. 'relative': if several feature values are present in one pixel interval, the mean value of all the feature values will be used for display. -render define the rendering effet of the feature track with plain the following values: 'plain': use plain color 'gradient': gradient value according to the feature value 'threshold': change color according to a threshold value -threshold define the threshold value to change color in none threshold rendering effect
Note: you cannot add several feature tracks. Other feature tracks will be discard.
add_element: add an existing element to an existing track. return O in case of error
$track->add_element($element)
get_track_name: return the start location of the map
$track_name = $track->get_track_name
get_track_type: return the track type (i.e. marker, interval or feature)
$track_type = $track->get_track_type
get_nb_elements: return the number of elements in a track
$nb_element = $track->get_nb_elements
get_list_element: return an ARRAY of the elements in the track
@List = $track->get_list_element
get_list_element_sorted_location: return an ARRAY of the elements in the track, sorted on their location
@List = $track->get_list_element_sorted_location
When your map and tracks object are created, then, you can create the elements you want to add into the tracks. There is three different type of object:
This object is primary designed to manage marker elements and to add them into a marker track. You will create it by passing the name (optional), the location of the element and the font color (optional, default=black).
my $marker = Chromosome::Map::Element->new( ... options ... ) Option Value Default ------ ----- ------- -name element name (optional) none -loc element location none -color color_name black
the -color tag will permit to define different element group and display them with different colors.
This object is primary designed to display chromosomal interval (i.e QTL region, genes, ...). This class is inherited from the element object with a field for the interval end location. You will create this object by passing it the block name (optional), block start and end location, and the block background color (note: the end location must be greater than thestart location).
my $block = Chromosome::Map::Bloc->new( ... options ... ) Option Value Default ------ ----- ------- -name block name (optional) none -loc block start location none -end block end location none -color color_name black
This object is designed to display chromosome features as %GC content, gene density or whatever features with a numerical value. This object is also inherited from the element class. You will create this object by passing it the feature location, the feature value, the value type (i.e. absolute or relative) and color, depending on the display rendering choosen during the feature track creation.
my $feature = Chromosome::Map::Feature->new( ... options ... ) Option Value Default ------ ----- ------- -loc feature location none -value feature value none -color feature rendering color softblue -threscolor feature threshold color (if value > threshold) red -value feature value 1 -valuetype feature value type: absolute 'absolute': absolute value (i.e. nb of genes) 'relative': relative value (i.e. %GC)
Of course, you cannot mix different value types in one track.
The choice of value type has an impact on the rendering of the feature track. You have to choose carefully the value type tag and the display tag of the feature track object:
If you choose an 'absolute' value type element, you can either display it in absolute or relative render option in the track object.
ex: let hypothetize you want to display the number of gene on your chromosome. For each gene, you will create a feature object:
my $gene = Chromosome::Map::Feature->new (-loc=$location);
Then, you can display the feature track as 'absolute': in one pixel interval, the number of genes will be displayed. But, you can also display the number of genes as a percentage of the maximum number of genes on the chromosome: the render tag in the track object have to be set to 'relative'.
If you choose a 'relative' value type element, you HAVE to set the render tag in the track object to 'relative' (since displaying relative data in an absolute is non sense).
Common public methods (available with element, block and feature objects):
get_element_loc:
$loc = $element->get_element_loc
get_element_name:
$element_name = $element->get_element_name
get_element_color:
$element_color = $element->get_element_color
Block public method:
get_block_end:
$block_end_location = $block->get_block_end
Feature public methods:
get_feature_value: return the value of the feature object
$value = $feature->get_feature_value
get_feature_value_type: return the type of the value (relative or absolute)
$value_type = $feature->get_feature_value_type
get_feature_threshold_color: return the threshold color (default=red)
$threshold_col = $feature->get_feature_threshold_color
Frédéric Lecerf http://chicken.genouest.org
Copyright (C) 2010, Frédéric Lecerf.
This module is free software; you can redistribute it or modify it under the same terms as Perl itself.
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To install Chromosome::Map, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Chromosome::Map
CPAN shell
perl -MCPAN -e shell install Chromosome::Map
For more information on module installation, please visit the detailed CPAN module installation guide.