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

NAME

       Bio::Graphics::Glyph::hybrid_plot - An xyplot plot drawing dual graph using data from two wiggle files per track

SYNOPSIS

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

DESCRIPTION

       Note that for full functionality this glyph requires Bio::Graphics::Glyph::generic (generic glyph is used for drawing individual matches
       for small RNA alignments at a high zoom level, specified by semantic zooming in GBrowse conf file) Unlike the regular xyplot, this glyph
       draws two overlapping graphs using value data in Bio::Graphics::Wiggle file format:

       track type=wiggle_0 name="Experiment" description="snRNA seq data" visibility=pack viewLimits=-2:2 color=255,0,0 altColor=0,0,255
       windowingFunction=mean smoothingWindow=16

	2L 400 500 0.5
	2L 501 600 0.5
	2L 601 700 0.4
	2L 701 800 0.1
	2L 800 900 0.1

       ##gff-version 3

       2L      Sample_rnaseq  rnaseq_wiggle 41	 3009 . . .
       ID=Samlpe_2L;Name=Sample;Note=YourNoteHere;wigfileA=/datadir/track_001.2L.wig;wigfileB=/datadir/track_002.2L.wig

       The "wigfileA" and "wigfileB" attributes give a relative or absolute pathname to Bio::Graphics::Wiggle format files for two concurrent sets
       of data. Basically, these wigfiles contain the data on signal intensity (counts) for sequences aligned with genomic regions. In wigfileA
       these data are additive, so for each sequence region the signal is calculated as a sum of signals from overlapping matches (signal). In
       wigfileB the signal represents the maximum value among all sequences (signal quality) aligned with the current region so the user can see
       the difference between accumulated signal from overlapping multiple matches (which may likely be just a noise from products of degradation)
       and high-quality signal from unique sequences.

       It is essential that wigfile entries in gff file do not have score, because score used to differentiate between data for dual graph and
       data for matches (individual features visible at higher magnification). After an update to wiggle_xyplot code colors for dual plot are now
       hard-coded (blue for signal and orange for signal quality). Alpha channel is also handled by wiggle_xyplot code now.

   OPTIONS
       In addition to some of the wiggle_xyplot glyph options, the following options are recognized:

	Name	    Value	 Description
	----	    -----	 -----------

	wigfileA    path name	 Path to a Bio::Graphics::Wiggle file for accumulated vales in 10-base bins

	wigfileB    path name	 Path to a Bio::Graphics::Wiggle file for max values in 10-base bins

	fasta	    path name	 Path to fasta file to enable BigWig drawing

	u_method    method name  Use method of [method name] to identify individual features (like alignment matches)
				 to show at high zoom level. By default it is set to 'match'

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

       Peter Ruzanov <pruzanov@oicr.on.ca>.

       Copyright (c) 2008 Ontario Institute for Cancer Research

       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::hybrid_plot(3pm)