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.\"
.IX Title "Bio::Graphics::Glyph::vista_plot 3pm"
.TH Bio::Graphics::Glyph::vista_plot 3pm "2019-11-25" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Graphics::Glyph::vista_plot \- The "vista_plot" glyph
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
See 
Bio::Graphics::Glyph, Bio::Graphics::Glyph::wiggle_xyplot and Bio::Graphics::Glyph::heat_map.
.SH "DESCRIPTION"
.IX Header "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'
.PP
\&\fBExample:\fR
.PP
2L  chip_seq  vista  5407   23011573  .  .  .  Name=ChipSeq Exp 1;wigfile=SomeWigFile.wigdb;peak_type=binding_site:exp1
.PP
The glyph will draw the wiggle file first, than overlay the peaks (if there are any)
over signal graph. Elsewhere in the \s-1GFF3\s0 file, there should be one or more features 
of type \*(L"binding_site:exp1\*(R", e.g.:
.PP
2L  exp1  binding_site  91934  92005  .  .  .
.PP
Options like 'balloon hover' and 'link' are available to customize
interaction with peaks in detail view.
.PP
\&\fBBigWig support:\fR
.PP
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
.PP
3L  chip_seq  vista   1    24543530  .  .  .   Name=ChipSeq Exp 2;wigfile=SomeBigWigFile.bw;peak_type=binding_site:exp2;fasta=YourOrganism.fasta
.PP
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 "\*(L" (i.e. peak_type=\*(R"")
In both cases, the stanza code will look the same (only essential parameters shown):
.PP
.Vb 10
\& [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
.Ve
.SH "OPTIONS"
.IX Header "OPTIONS"
Options are the same as for wiggle_xyplot and heat_map
.PP
\&\fBAdditional parameters:\fR
.PP
\&\fBalpha\fR
set transparency for peak area.
.PP
\&\fBglyph_subtype\fR
Display only 'peaks', 'signal', 'density' or 'peaks+signal'. 
Aliases for 'peaks+signal' include \*(L"both\*(R" and \*(L"vista\*(R".
.PP
\&\fBRecommended global settings:\fR
.PP
for proper peak drawing transparency should be enabled
by setting 
\&\fBtruecolors=1\fR 
in \fIGBrowse.conf\fR file
.SH "BUGS"
.IX Header "BUGS"
Please report them.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Graphics::Panel
Bio::Graphics::Glyph
Bio::Graphics::Glyph::wiggle_xyplot
Bio::Graphics::Glyph::heat_map
\&\s-1GD\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Peter Ruzanov pruzanov@oicr.on.ca
.PP
Copyright (c) 2010 Ontario Institute for Cancer Research
.PP
.Vb 5
\& 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.
.Ve