Bio::Graphics::Glyph::hybrid_plot - An xyplot plot drawing dual graph using data
from two or more wiggle files per track
See <Bio::Graphics::Panel> <Bio::Graphics::Glyph> and
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
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
2L Sample_rnaseq rnaseq_wiggle 41 3009 . . .
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
In addition to some of the wiggle_xyplot glyph options, the following options
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'
Please report them.
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow,
Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
Peter Ruzanov <email@example.com>.
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.