Bio::Graphics::Glyph::wiggle_xyplot(3pm)		User Contributed Perl Documentation		  Bio::Graphics::Glyph::wiggle_xyplot(3pm)

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).

   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)

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.

perl v5.14.2							    2012-02-20				  Bio::Graphics::Glyph::wiggle_xyplot(3pm)