Bio::Graphics::Glyph::vista_plot(3pm)			User Contributed Perl Documentation		     Bio::Graphics::Glyph::vista_plot(3pm)

NAME

       Bio::Graphics::Glyph::vista_plot - The "vista_plot" glyph

SYNOPSIS

       See Bio::Graphics::Glyph, Bio::Graphics::Glyph::wiggle_xyplot and Bio::Graphics::Glyph::heat_map.

DESCRIPTION

       This glyph draws peak calls (features with discreet boundaries, i.e. putative transcription sites, over signal graph (wiggle_xyplot)
       requires a special load gff file that uses attributes 'wigfile' and 'peak_type'

       Example:

       2L  chip_seq  vista  5407   23011573  .	.  .  Name=ChipSeq Exp 1;wigfile=SomeWigFile.wigdb;peak_type=binding_site:exp1

       The glyph will draw the wiggle file first, than overlay the peaks (if there are any) over signal graph. Elsewhere in the GFF3 file, there
       should be one or more features of type "binding_site:exp1", e.g.:

       2L  exp1  binding_site  91934  92005  .	.  .

       Options like 'balloon hover' and 'link' are available to customize interaction with peaks in detail view.

       BigWig support:

       Supported bigwig format also requires another attribute to be supplied in load gff file (fasta) which specifies sequence index file for the
       organism in use. The data file should have the 'bw' extension - it is used to detect the BigWig format by vista_plot

       3L  chip_seq  vista   1	  24543530  .  .  .   Name=ChipSeq Exp
       2;wigfile=SomeBigWigFile.bw;peak_type=binding_site:exp2;fasta=YourOrganism.fasta

       Note that all attributes should be present in load gff, as the code currently does not handle situation when only some of the attributes
       are in gff. To omit peak or signal drawing use "" (i.e. peak_type="") In both cases, the stanza code will look the same (only essential
       parameters shown):

	[VISTA_PLOT]
	feature 	= vista:chip_seq
	glyph		= vista_plot
	label		= 1
	smoothing	= mean
	smoothing_window = 10
	bump density	= 250
	autoscale	= local
	variance_band	= 1
	max_peak	= 255
	min_peak	= 1
	peakwidth	= 3
	start_color	= lightgray
	end_color	= black
	pos_color	= blue
	neg_color	= orange
	bgcolor 	= orange
	alpha		= 80
	fgcolor 	= black
	database	= database_with_load_gff_data
	box_subparts	= 1
	bicolor_pivot	= min
	key		= VISTA plot

OPTIONS

       Options are the same as for wiggle_xyplot and heat_map

       Additional parameters:

       alpha set transparency for peak area.

       glyph_subtype Display only 'peaks', 'signal', 'density' or 'peaks+signal'.  Aliases for 'peaks+signal' include "both" and "vista".

       Recommended global settings:

       for proper peak drawing transparency should be enabled by setting truecolors=1 in GBrowse.conf file

BUGS

       Please report them.

SEE ALSO

       Bio::Graphics::Panel Bio::Graphics::Glyph Bio::Graphics::Glyph::wiggle_xyplot Bio::Graphics::Glyph::heat_map GD

AUTHOR

       Peter Ruzanov pruzanov@oicr.on.ca

       Copyright (c) 2010 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 v5.14.2							    2012-02-20				     Bio::Graphics::Glyph::vista_plot(3pm)