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=1312The "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.