Manual Reference Pages - BIO::GRAPHICS::GLYPH::HYBRID_PLOT (3)
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 <Bio::Graphics::Glyph::wiggle_xyplot>.
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
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.
In addition to some of the wiggle_xyplot glyph options, the following options are
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.
Peter Ruzanov <firstname.lastname@example.org>.
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.
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