Bio::Graphics::Glyph::spectrogram - The "spectrogram" glyph
See L<Bio::Graphics::Panel>, L<Bio::Graphics::Glyph>
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
The entire 2D spectrogram is a series of unaggregated, unbumped 1D spectrogram
The spectrogram glyph assigns colors using the HSV color space, where an angular
coordinate for hue is assigned to each base (G yellow ; A blue ; C
green ; 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.
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
Please report them.
Sheldon McKay <email@example.com>.
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.