Bio::Graphics::Glyph::vista_plot - The "vista_plot" glyph
See Bio::Graphics::Glyph, Bio::Graphics::Glyph::wiggle_xyplot and
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
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
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):
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 are the same as for wiggle_xyplot and heat_map
set transparency for peak area.
Display only 'peaks', 'signal', 'density' or
'peaks+signal'. Aliases for 'peaks+signal' include "both" and
Recommended global settings:
for proper peak drawing transparency should be enabled by setting
Please report them.
Bio::Graphics::Panel Bio::Graphics::Glyph Bio::Graphics::Glyph::wiggle_xyplot
Peter Ruzanov firstname.lastname@example.org
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.