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.