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MassSpec::ViewSpectrum 0.05
MassSpec::ViewSpectrum is a Perl extension for viewing a mass spectrum. more>>
MassSpec::ViewSpectrum is a Perl extension for viewing a mass spectrum.
SYNOPSIS
use MassSpec::ViewSpectrum;
open PNG, ">mygraphic.png" or die "Unable to open output filen";
binmode PNG;
my @masses = (1036.4,1133,1437,1480,1502);
my @intensities = (0.1,0.15,0.05,0.10,0.2);
my @annotations = (b,w,internal w, ,internal y);
my $vs = MassSpec::ViewSpectrum->new(@masses,@intensities, @annotations);
$vs->set(yaxismultiplier => 1.8); # a sample tweak to adjust the output
my $output = $vs->plot();
print PNG $output;
close PNG;
MassSpec::ViewSpectrum - Perl extension for viewing a mass spectrum, e.g. typically obtained from the fragmentation of proteins or peptides.
At present this is only implemented using GD graphics, but in principle this could be subclassed in the future to include alternative graphic paradigms such as SVG and Tk.
The current implementation uses a mixture of GD::Graph and native GD, since GD::Graph 1.43 fails to draw the required vertical lines correctly.
Negative peak intensity values are permitted; this permits the drawing of "pseudospectra" which, for example, illustrate peaks present in one spectrum but missing in another.
<<lessSYNOPSIS
use MassSpec::ViewSpectrum;
open PNG, ">mygraphic.png" or die "Unable to open output filen";
binmode PNG;
my @masses = (1036.4,1133,1437,1480,1502);
my @intensities = (0.1,0.15,0.05,0.10,0.2);
my @annotations = (b,w,internal w, ,internal y);
my $vs = MassSpec::ViewSpectrum->new(@masses,@intensities, @annotations);
$vs->set(yaxismultiplier => 1.8); # a sample tweak to adjust the output
my $output = $vs->plot();
print PNG $output;
close PNG;
MassSpec::ViewSpectrum - Perl extension for viewing a mass spectrum, e.g. typically obtained from the fragmentation of proteins or peptides.
At present this is only implemented using GD graphics, but in principle this could be subclassed in the future to include alternative graphic paradigms such as SVG and Tk.
The current implementation uses a mixture of GD::Graph and native GD, since GD::Graph 1.43 fails to draw the required vertical lines correctly.
Negative peak intensity values are permitted; this permits the drawing of "pseudospectra" which, for example, illustrate peaks present in one spectrum but missing in another.
Download (0.007MB)
Added: 2006-08-30 License: Perl Artistic License Price:
1153 downloads
MassSpec::ViewSpectrum::RealVsHypPeptide 0.02
MassSpec::ViewSpectrum::RealVsHypPeptide is a Perl module to view a real mass spectrum on the same graph. more>>
MassSpec::ViewSpectrum::RealVsHypPeptide is a Perl module to view a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico.
SYNOPSIS
use MassSpec::ViewSpectrum::RealVsHypPeptide;
open GRAPHIC, ">mygraphic.png" or die "Unable to open output filen";
binmode GRAPHIC;
my @masses = (78.1,81.1,81.7,85.4,86.8,88.8,89.4,97.6,99.0,99.4,108.7,112.1,129.1,
130.1,132.1,147.7,157.1,158.1,159.1,169.1,171.1,175.1,187.1,229.1,246.2,258.1,
266.0,327.2,328.2,345.2,415.2,426.2,432.2,531.2,559.3,623.4,639.3,643.3,644.4,
645.0,647.5,686.4,687.4,689.4);
my @intensities = (8.7,7.7,7.3,10.5,7.7,7.3,8.4,8.0,9.1,9.1,7.3,29.0,12.6,7.3,8.0,
7.7,11.9,9.8,10.1,7.3,10.5,131.0,9.4,50.3,22.7,44.7,16.8,30.4,18.2,53.1,25.5,
15.7,7.7,14.0,46.8,38.4,7.3,11.5,8.7,7.3,8.7,7.3,24.8,194.2);
my $peptide = "RTSVAR";
my $vs = MassSpec::ViewSpectrum::RealVsHypPeptide->new($peptide, @masses,@intensities);
$vs->set(yaxismultiplier => 1.8); # a sample tweak to adjust the output
$vs->set(title => "BSA-689 -- " . $peptide);
my $output = $vs->plot();
print GRAPHIC $output;
close GRAPHIC;
MassSpec::ViewSpectrum::RealVsHypPeptide - View a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico. The in silico fragmention is performed by generating all of the possible peptides which contain either the amino-terminal or carboxyl-terminal amino acids.
Negative peak intensity values are permitted; this permits the drawing of "pseudospectra" which, for example, illustrate peaks present in one spectrum but missing in another. Note that these negative peaks have no true intensities, but in some cases we assign different heights to illustrate the differences among different hypothetical peaks. In addition, pseudocoloring of both positive and negative peaks is performed to illustrate what type of ion that peak represents. In some cases these ions are labelled explicitly, although in practice it is best to minimize this labelling to avoid excessive clutter.
<<lessSYNOPSIS
use MassSpec::ViewSpectrum::RealVsHypPeptide;
open GRAPHIC, ">mygraphic.png" or die "Unable to open output filen";
binmode GRAPHIC;
my @masses = (78.1,81.1,81.7,85.4,86.8,88.8,89.4,97.6,99.0,99.4,108.7,112.1,129.1,
130.1,132.1,147.7,157.1,158.1,159.1,169.1,171.1,175.1,187.1,229.1,246.2,258.1,
266.0,327.2,328.2,345.2,415.2,426.2,432.2,531.2,559.3,623.4,639.3,643.3,644.4,
645.0,647.5,686.4,687.4,689.4);
my @intensities = (8.7,7.7,7.3,10.5,7.7,7.3,8.4,8.0,9.1,9.1,7.3,29.0,12.6,7.3,8.0,
7.7,11.9,9.8,10.1,7.3,10.5,131.0,9.4,50.3,22.7,44.7,16.8,30.4,18.2,53.1,25.5,
15.7,7.7,14.0,46.8,38.4,7.3,11.5,8.7,7.3,8.7,7.3,24.8,194.2);
my $peptide = "RTSVAR";
my $vs = MassSpec::ViewSpectrum::RealVsHypPeptide->new($peptide, @masses,@intensities);
$vs->set(yaxismultiplier => 1.8); # a sample tweak to adjust the output
$vs->set(title => "BSA-689 -- " . $peptide);
my $output = $vs->plot();
print GRAPHIC $output;
close GRAPHIC;
MassSpec::ViewSpectrum::RealVsHypPeptide - View a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico. The in silico fragmention is performed by generating all of the possible peptides which contain either the amino-terminal or carboxyl-terminal amino acids.
Negative peak intensity values are permitted; this permits the drawing of "pseudospectra" which, for example, illustrate peaks present in one spectrum but missing in another. Note that these negative peaks have no true intensities, but in some cases we assign different heights to illustrate the differences among different hypothetical peaks. In addition, pseudocoloring of both positive and negative peaks is performed to illustrate what type of ion that peak represents. In some cases these ions are labelled explicitly, although in practice it is best to minimize this labelling to avoid excessive clutter.
Download (0.008MB)
Added: 2007-02-23 License: Perl Artistic License Price:
974 downloads
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