|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'
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.
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
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 email@example.com
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.