Reference

Bio::Graphics::Glyph::wiggle_xyplot(3pm)

An xyplot plot compatible with dense "wig"data

NAME

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

SYNOPSIS

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

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).

The glyph also supports features which offer a statistical_summary() method, such as those from Bio::DB::BigWig. This method returns a hash of values, including validCount, maxVal, minVal, sumData, and sumSquares. For each interval, a statistical score is generated from these values. The mean, minimum, maximum, or sum of the values may be reported.

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.
   interval_method   method  When working with bigWig features that use the
                             statistical_summary() method, define the method
                             for reporting one or more scores within each
                             interval. Options include "mean", "sum", "min",
                             or "max". Default is "mean".

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)

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 <[email protected]>.

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.

History