Provided by: libbio-graphics-perl_2.40-3_all bug

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.

          autoscale   "local" or "global"
                                    If one or more of min_score and max_score options
                                    are absent, then these values will be calculated
                                    automatically. The "autoscale" option controls how
                                    the calculation is done. The "local" value will
                                    scale values according to the minimum and maximum
                                    values present in the window being graphed. "global"
                                    will use chromosome-wide statistics for the entire
                                    wiggle or dense file to find min and max values.

          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.