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Bio::Graphics::Glyph::wiggle_density.3pm

NAME

Bio::Graphics::Glyph::wiggle_density - A density plot compatible with dense "wig"data

SYNOPSIS

   See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>.
 
 

DESCRIPTION

This glyph works like the regular density but takes value data in Bio::Graphics::Wiggle file format:

  reference = chr1
  ChipCHIP Feature1 1..10000 wigfile=./test.wig;wigstart=0
  ChipCHIP Feature2 10001..20000 wigfile=./test.wig;wigstart=656
  ChipCHIP Feature3 25001..35000 wigfile=./test.wig;wigstart=1312
 
 

The ``wigfile'' attribute gives a relative or absolute pathname to a Bio::Graphics::Wiggle format file. The optional ``wigstart'' option gives the offset to the start of the data. If not specified, a linear search will be used to find the data. The data consist of a packed binary representation of the values in the feature, using a constant step such as present in tiling array data.

OPTIONS

The same as the regular graded_segments glyph, except that the following options are recognized:

    Name        Value        Description
    ----        -----        -----------
 
    basedir     path         Path to be used to resolve "wigfile" and "densefile"
                                 tags giving relative paths. Default is to use the
                                 current working directory. Absolute wigfile &
                                 densefile paths will not be changed.
 
    smoothing   method name  Smoothing method: one of "mean", "max", "min" or "none"
 
    smoothing_window 
                integer      Number of values across which data should be smoothed.
 
    bicolor_pivot
                name         Where to pivot the two colors when drawing bicolor plots.
                                Options are "mean" and "zero". A numeric value can
                                also be provided.
 
    pos_color   color        When drawing bicolor plots, the fill color to use for values
                               that are above the pivot point.
 
    neg_color   color        When drawing bicolor plots, the fill color to use for values
                               that are below the pivot point.
 
 

SPECIAL FEATURE TAGS

The glyph expects one or more of the following tags (attributes) in feature it renders:

    Name        Value        Description
    ----        -----        -----------
 
    wigfile     path name    Path to the Bio::Graphics::Wiggle file for vales.
                             (required)
 
    densefile   path name    Path to a Bio::Graphics::DenseFeature object
                                (deprecated)
 
    denseoffset integer      Integer offset to where the data begins in the
                                Bio::Graphics::DenseFeature file (deprecated)
 
    densesize   integer      Integer size of the data in the Bio::Graphics::DenseFeature
                                file (deprecated)
 
 

BUGS

Please report them.

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::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::allele_tower, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD

AUTHOR

Lincoln Stein <steinl@cshl.edu>.

Copyright (c) 2007 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.