NAME
Chromosome::Map - Generate GD images of chromosome maps
SYNOPSIS
#!/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;DESCRIPTION
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
METHODS
This section describes the class and object methods for the Chromosome::Map module.
Map object
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 40Public 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->pngget_map_name: return the title name of the map
$name = $map->get_map_nameget_map_start: return the start location of the map
$map_start = $map->get_map_startget_map_size: return the end location of the map (i.e. the map size)
$map_size = $map->get_map_sizeget_map_units: return the unit of the map (i.e. cM, MB, KB...)
$map_unit = $map->get_map_unitsget_nb_tracks: return the number of the tracks in the map
$nb_track = $map->get_nb_tracksget_list_track: return a list (%Hash) of the tracks in the map
%List = $map->get_list_track
Track object
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 effectNote: you cannot add several feature tracks. Other feature tracks will be discard.
Public methods description:
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_nameget_track_type: return the track type (i.e. marker, interval or feature)
$track_type = $track->get_track_typeget_nb_elements: return the number of elements in a track
$nb_element = $track->get_nb_elementsget_list_element: return an ARRAY of the elements in the track
@List = $track->get_list_elementget_list_element_sorted_location: return an ARRAY of the elements in the track, sorted on their location
@List = $track->get_list_element_sorted_location
Element, Block and Feature objects
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:
- Element 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 blackthe -color tag will permit to define different element group and display them with different colors.
- Block object
-
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 - Feature object
-
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_locget_element_name:
$element_name = $element->get_element_nameget_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_valueget_feature_value_type: return the type of the value (relative or absolute)
$value_type = $feature->get_feature_value_typeget_feature_threshold_color: return the threshold color (default=red)
$threshold_col = $feature->get_feature_threshold_color
AUTHOR
Frédéric Lecerf http://chicken.genouest.org
COPYRIGHT
Copyright (C) 2010, Frédéric Lecerf.
LICENSE
This module is free software; you can redistribute it or modify it under the same terms as Perl itself.
1 POD Error
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- Around line 820:
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