NAME

       Bio::Graphics::Glyph::hybrid_plot - An xyplot plot drawing dual graph using data from two
       or more 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.

       For a third wiggle file use the attribute "wigfileC" and so forth.

       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.