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.

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>.