Lincoln D. Stein
and 1 contributors

NAME

Bio::Graphics::Glyph::hybrid_plot - An xyplot plot drawing dual graph using data from two wiggle files per track

SYNOPSIS

See <Bio::Graphics::Panel> <Bio::Graphics::Glyph> and <Bio::Graphics::Glyph::xyplot>.

DESCRIPTION

Note that for full functionality this glyph requires Bio::Graphics::Glyph::box (box 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. In wigfileB the signal represents the maximum value among all sequences aligned with the current region so the user can see the difference between accumulated signal from overlapping multiple matches (which may likely be just noise from products of degradation) and signal from unique sequences. 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)

OPTIONS

In addition to some of the 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

 pos_color   color        When drawing bicolor plots, the fill color to use for max values
                                                                                                                                                                                                              neg_color   color        When drawing bicolor plots, the fill color to use for total (accumulated) values
        
 alpha       number       For blending colors ofthe overlapping graphs (between 1 and 127) truecolor must be enabled

 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.