Bio::Graphics::Glyph::wiggle_box(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::wiggle_box(3pm)
NAME
Bio::Graphics::Glyph::wiggle_box - A generic box glyph compatible with dense "wig"data
SYNOPSIS
See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>.
DESCRIPTION
This glyph works like the regular 'box' glyph 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.
This glyph is intended for dense, qualitative feature data. Any score data for each data point is only evaluated for true/false, when
true, a box of the specified bgcolor is drawn, when false, nothing is drawn. No data smoothing is used.
Two primary benefits of using this glyph (with wiggle data) are:
1) For large, genome-wide data sets, the speed of panel rendering is
greatly improved.
2) Large sets of related features can be rendered as a UCSC-style subtrack
without the need for aggregation or a GFF3 containment hierarchy.
A disadvantage to this approach is that individual features will have no attributes associated with them and will appear as anonymous
blocks within a sub-track.
An example use for this glyph is annotated transcribed regions from microarray experiments. Such regions are identified based on raw
microarray data but do not necessarily have a score associated with them. In this case, using the wiggle_box glyph provides a graphical
summary of an expression array experiment.
DATA
The wiggle data used for this glyph should be loaded using the 'BED' format in order to allow features of variable width. The fourth
column should be a true value, with numeric or ".". An example is shown below:
track type=wiggle_0 name="transfrags" description="D. melanogaster transcribed fragments 0-2hrs"
2L 9309 9451 1
2L 10697 11021 1
2L 11101 11345 1
2L 11410 11521 1
2L 11771 12243 1
2L 12314 12954 1
2L 13516 15746 1
2L 17033 17191 1
2L 18232 18580 1
2L 19860 19999 1
OPTIONS
This glyph accepts the standard generic option set. It differs in that the label and description and title/mouseover labels apply to the
whole, panel-wide sub-track feature rather than to individual boxes.
See Bio::Graphics::Glyph::wiggle_xyplot for a description of the wiggle-specific options and data formats.
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
Sheldon McKay <mckays@cshl.edu>.
Copyright (c) 2008 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_box(3pm)