Bio::Graphics::Glyph::wiggle_xyplot - An xyplot plot compatible with dense "wig"data

- NAME
- SYNOPSIS
- DESCRIPTION

- OPTIONS
- SPECIAL FEATURE TAGS

- BUGS
- SEE ALSO
- AUTHOR

# NAME

Bio::Graphics::Glyph::wiggle_xyplot - An xyplot plot compatible with dense "wig"data

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# SYNOPSIS

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

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# DESCRIPTION

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

     reference = chr1
     ChipCHIP Feature1 1..10000 wigfile=./test.wig
     ChipCHIP Feature2 10001..20000 wigfile=./test.wig
     ChipCHIP Feature3 25001..35000 wigfile=./test.wig

The "wigfile" attribute gives a relative or absolute pathname to a Bio::Graphics::Wiggle format file. 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. Wigfiles are created using the Bio::Graphics::Wiggle module or the wiggle2gff3.pl script, currently both part of the gbrowse package.

Alternatively, you can place an array of quantitative data directly in the "wigdata" attribute. This can be an arrayref of quantitative data starting at feature start and ending at feature end, or the data string returned by Bio::Graphics::Wiggle->export_to_wif64($start,$end).

## OPTIONS

In addition to all the xyplot glyph options, 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.

       variance_band boolean    If true, draw a grey band across entire plot showing mean
                                   and +/- 1 standard deviation (for wig files only).

       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 or object
                                for quantitative values.

       wigdata     string       Data exported from a Bio::Graphics::Wiggle in WIF
                                format using its export_to_wif64() method.

       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)

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# BUGS

Please report them.

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# SEE ALSO

the Bio::Graphics::Panel manpage, the Bio::Graphics::Glyph manpage, the Bio::Graphics::Glyph::arrow manpage, the Bio::Graphics::Glyph::cds manpage, the Bio::Graphics::Glyph::crossbox manpage, the Bio::Graphics::Glyph::diamond manpage, the Bio::Graphics::Glyph::dna manpage, the Bio::Graphics::Glyph::dot manpage, the Bio::Graphics::Glyph::ellipse manpage, the Bio::Graphics::Glyph::extending_arrow manpage, the Bio::Graphics::Glyph::generic manpage, the Bio::Graphics::Glyph::graded_segments manpage, the Bio::Graphics::Glyph::heterogeneous_segments manpage, the Bio::Graphics::Glyph::line manpage, the Bio::Graphics::Glyph::pinsertion manpage, the Bio::Graphics::Glyph::primers manpage, the Bio::Graphics::Glyph::rndrect manpage, the Bio::Graphics::Glyph::segments manpage, the Bio::Graphics::Glyph::ruler_arrow manpage, the Bio::Graphics::Glyph::toomany manpage, the Bio::Graphics::Glyph::transcript manpage, the Bio::Graphics::Glyph::transcript2 manpage, the Bio::Graphics::Glyph::translation manpage, the Bio::Graphics::Glyph::allele_tower manpage, the Bio::DB::GFF manpage, the Bio::SeqI manpage, the Bio::SeqFeatureI manpage, the Bio::Das manpage, GD

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# 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.

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Bio::Graphics::Glyph::wiggle_xyplot - An xyplot plot compatible with dense "wig"data