NAME¶
Bio::Graphics::Glyph::trace - A glyph that visualizes a trace file
SYNOPSIS¶
use Bio::Graphics;
use Bio::Seq;
use Bio::SeqFeature::Generic;
my $bsg = 'Bio::SeqFeature::Generic';
my $seq = Bio::Seq->new(-length=>1000);
my $whole = $bsg->new(-display_name => 'Clone82',
-start => 1,
-end => $seq->length);
my $trace1 = $bsg->new(-start => 100,
-end => 300,
-display_name => 'Excretory System',
-tag=>{
trace=>"/path/to/trace/file.scf"
}
);
my $trace2 = $bsg->new(-start => 500,
-end => 800,
-display_name => 'Expression Pattern',
-tag=>{
trace=>"http://localhost/traces/file2.scf"
}
);
my $panel = Bio::Graphics::Panel->new(-length => $seq->length,
-width => 800,
-truecolor => 1,
-key_style => 'between',
-pad_left => 10,
-pad_right => 10,
);
$panel->add_track($whole,
-glyph => 'arrow',
-double => 1,
-tick => 2,
-label => 1,
);
$panel->add_track([$trace1,$trace2],
-glyph => 'trace',
-label => 1,
-key => 'Example traces');
binmode STDOUT;
print $panel->png;
DESCRIPTION¶
This glyph parses and displays trace information from a file. A generic glyph is
used to show where the trace is located and when the display is zoomed in
enough to see the sequence, the trace will be drawn.
The trace file can only be in SCF format. The file can be located on the local
filesystem or located at a remote URL (provided that you have the LWP module
installed).
Until an alignment feature is added to this glyph, the feature start and end
must correspond exactly with the begining and end of the called sequence.
Meaning that even if the starting sequence is poor and doesn't match the
sequence, it must still be included.
The figure below illustrates this. The trace and the reference sequence align
from points "b" to "c". The positions "A" and
"D" need to be calculated and used in order for the trace to line up
correctly.
A b c D
ref -------------------------------------------------
|||||||||||
trace ------------------------
The glyph may be modified in the future to avoid this hassle (and it should
still be compatible with the method described above).
OPTIONS¶
The following options are standard among all Glyphs. See Bio::Graphics::Glyph
for a full explanation.
Option Description Default
------ ----------- -------
-fgcolor Foreground color black
-outlinecolor Synonym for -fgcolor
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Glyph font gdSmallFont
-connector Connector type 0 (false)
-connector_color
Connector color black
-label Whether to draw a label 0 (false)
-description Whether to draw a description 0 (false)
-hilite Highlight color undef (no color)
The following additional options are available to the "image" glyph:
Option Description Default
------ ----------- -------
-trace Specify the trace path or URL none
to use for this feature
-trace_prefix String to prepend to none
each trace path. You may prepend
a directory or a partial URL.
-trace_height The height in pixels that the 90
trace will be drawn
-vertical_spacing Vertical distance from the box 20
that shows the physical span of
the feature to the top of the
picture (in pixels)
-glyph_delegate Glyph to use when zoomed out too 'generic'
far for the trace to be drawn
-a_color Color of the line representing 'green'
Adenine on the trace
-c_color Color of the line representing 'blue'
Cytosine on the trace
-g_color Color of the line representing 'black'
Guanine on the trace
-t_color Color of the line representing 'red'
Thymine on the trace
-show_border Show the black border from 0
around the trace
-abi_scale The scale factor for abi 1
formatted files. This is
multiplied against the max
trace value to determine the
hight of peaks.
Specifying the Trace¶
The path to the trace file can be specified in two ways. First, you can place it
in the feature itself using a tag named "trace". Second, you can
specify it as a track option using a callback:
$panel->add_track(\@features,
-glyph=>'trace',
-trace => sub { my $feature = shift;
my $trace_path = do_something();
return $trace }
);
You can of course give -trace a constant string, in which case each feature will
show the same trace.
The trace can be a file on the local operating system or a URL. However, URL
fetching will only work if the LWP module is installed on your system.
Otherwise the glyph will fail with an error message.
If the trace is a relative path (it does not begin with a slash or a URL
protocol), then the contents of -trace_prefix will be prepended to it. This
allows you to specify traces that are relative to a particular directory or a
partial URL. Example:
$panel->add_track(\@features,
-glyph => 'trace',
-trace_prefix => 'http://localhost/anatomy/trace-browser_files',
);
This specifies that each feature's "trace" tag is to be appended to
the partial localhost URL, thereby saving space.
Glyph Delegation¶
The trace glyph consists of two parts: an upper part that shows the extent of
the feature in base pair coordinates, and a lower part that shows the trace.
The upper part will always be displayed. The lower part will only display if
zoomed close enough to see the sequence.
By default the upper part uses the "generic" glyph, which is a simple
rectangle filled with the bgcolor and outlined with the fgcolor. To use a
different glyph in the upper part, specify the -glyph_delegate option, giving
the name of the glyph you wish to use. For instance, to use the
"span" glyph:
$panel->add_track(\@features,
-glyph => 'trace',
-glyph_delegate => 'span'
);
This feature does not work with all glyphs, and in particular requires a recent
CVS checkout of Bio::Perl to work properly with the "arrow",
"span" and "primers" glyphs (support for the feature did
not make it into version 1.5).
BUGS AND LIMITATIONS¶
See the DESCRIPTION for an explaination of how to align the trace with the
reference.
The trace looks a little off when the feature is on the negative strand of the
reference. This is because the letters are on the oppisite side of the
position line. This issue should be addressed.
This glyph uses it's own version of the Bio::Graphics::Panel method,
map_pt(), due to that method not behaving as needed. The new copied
method is called "trace_map_pt".
If the trace file is gzipped, it will unzip it without destroying the gzipped
file. However, it will also not remove the newly created file. This will only
be an issue when the files are stored locally, since web accessed trace files
are stored as temp files anyway.
SEE ALSO¶
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow,
Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna,
Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic,
Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::image,
Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion,
Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::rndrect,
Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow,
Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript,
Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation,
Bio::Graphics::Glyph::triangle, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI,
Bio::Das, GD
AUTHOR¶
Ben Faga <faga@cshl.edu>, Lincoln Stein <lstein@cshl.org>, Todd
Harris <harris@cshl.org>
Copyright (c) 2006 Cold Spring Harbor Laboratory
This package and its accompanying libraries is free software; you can
redistribute it and/or modify it under the terms of the GPL (either version 1,
or at your option, any later version) or the Artistic License 2.0. Refer to
LICENSE for the full license text. In addition, please see DISCLAIMER.txt for
disclaimers of warranty.