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Bio::Graphics::Glyph::UseriContributed PerBio::Graphics::Glyph::hybrid_plot(3)

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.

perl v5.32.0			  2020-08-Bio::Graphics::Glyph::hybrid_plot(3)

NAME | SYNOPSIS | DESCRIPTION | BUGS | SEE ALSO | AUTHOR

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