Bio::Graphics::Glyph::spectrogram man page on Pidora

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Bio::Graphics::Glyph::UsertContributed PerBio::Graphics::Glyph::spectrogram(3)

NAME
       Bio::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 v5.14.1			  2011-07-Bio::Graphics::Glyph::spectrogram(3)
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