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Bio::Graphics::Glyph::UseraContributed PerlBio::Graphics::Glyph::vista_plot(3)

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 v5.32.1			  2021-11-0Bio::Graphics::Glyph::vista_plot(3)

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

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