Bio::Graphics::Glyph::UsertContributed PerBio::Graphics::Glyph::spectrogram(3)NAMEBio::Graphics::Glyph::spectrogram - The "spectrogram" glyph
SYNOPSIS
See L<Bio::Graphics::Panel>, L<Bio::Graphics::Glyph>
and L<Bio::Graphics::Browser::Plugin::Spectrogram>
DESCRIPTION
This glyph is designed to draw DNA spectrograms for the Spectrogram
plugin. It is not meant to be used as a standalone glyph and has few
public options. Most of the glyph's behavior is controlled via the
spectrogram plugin.
The glyph expects unaggregated 1D spectrogram features, each of which
is a vertical column, with one row for each integer frequency. The
number of frequencies is controlled by the window size and/or the
Spectrogram plugin. The width of the feature corresponds to the size
of the overlap between adjacent windows. The values for each frequency
are in four channels, one for each base. The color of each row
("spot") represents the dominant base(s) and the intensity represents
the magnitude of the signal at that frequency
The entire 2D spectrogram is a series of unaggregated, unbumped 1D
spectrogram features.
The spectrogram glyph assigns colors using the HSV color space, where
an angular coordinate for hue is assigned to each base (G yellow [60];
A blue [240]; C green [120]; T red[0/360]). The saturation value is
fixed at the maximum of 100 and the brightness value is scaled
according to the magnitude for each frequency, ranging from black to
the pure hue.
The hue is determined in one of two ways:
If the signal for one base is dominant (> 50% of total for the four
channels) the angular coordinate for that base is used. The brightness
is calculated using the total signal from all four channels.
If no base has a dominant signal, the weighted average angular
coordinate is calculated using the relative contribution from each
channel. The brightness is calculated from the total signal from all
four channels.
The y-axis labels require at least 40 pixels of left-padding. They
will be truncated if less than 40 of padding is specified in the
configuration file.
OPTIONS
The following standard options are accepted:
Option Description Default
------------------------
-height Height of glyph calculated
-bump Whether to bump features off
The following glyph-specific options are also used:
-win window size used to calculate calculated
the spectrogram values
BUGS
Please report them.
AUTHOR
Sheldon McKay <mckays@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.
perl v5.14.12011-07-Bio::Graphics::Glyph::spectrogram(3)