See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>.
DESCRIPTIONThis glyph works like the regular xyplot but takes value data in Bio::Graphics::Wiggle file format:
reference = chr1 ChipCHIP Feature1 1..10000 wigfile=./test.wig ChipCHIP Feature2 10001..20000 wigfile=./test.wig ChipCHIP Feature3 25001..35000 wigfile=./test.wig
The ``wigfile'' attribute gives a relative or absolute pathname to a Bio::Graphics::Wiggle format file. The data consist of a packed binary representation of the values in the feature, using a constant step such as present in tiling array data. Wigfiles are created using the Bio::Graphics::Wiggle module or the wiggle2gff3.pl script, currently both part of the gbrowse package.
Alternatively, you can place an array of quantitative data directly in the ``wigdata'' attribute. This can be an arrayref of quantitative data starting at feature start and ending at feature end, or the data string returned by Bio::Graphics::Wiggle->export_to_wif64($start,$end).
The glyph also supports features which offer a statistical_summary() method, such as those from Bio::DB::BigWig. This method returns a hash of values, including validCount, maxVal, minVal, sumData, and sumSquares. For each interval, a statistical score is generated from these values. The mean, minimum, maximum, or sum of the values may be reported.
OPTIONSIn addition to all the xyplot glyph options, the following options are recognized:
Name Value Description ---- ----- ----------- basedir path Path to be used to resolve "wigfile" and "densefile" tags giving relative paths. Default is to use the current working directory. Absolute wigfile & densefile paths will not be changed. autoscale "local" or "global" If one or more of min_score and max_score options are absent, then these values will be calculated automatically. The "autoscale" option controls how the calculation is done. The "local" value will scale values according to the minimum and maximum values present in the window being graphed. "global" will use chromosome-wide statistics for the entire wiggle or dense file to find min and max values. smoothing method name Smoothing method: one of "mean", "max", "min" or "none" smoothing_window integer Number of values across which data should be smoothed. variance_band boolean If true, draw a grey band across entire plot showing mean and +/- 1 standard deviation (for wig files only). bicolor_pivot name Where to pivot the two colors when drawing bicolor plots. Options are "mean" and "zero". A numeric value can also be provided. pos_color color When drawing bicolor plots, the fill color to use for values that are above the pivot point. neg_color color When drawing bicolor plots, the fill color to use for values that are below the pivot point. interval_method method When working with bigWig features that use the statistical_summary() method, define the method for reporting one or more scores within each interval. Options include "mean", "sum", "min", or "max". Default is "mean".
SPECIAL FEATURE TAGSThe glyph expects one or more of the following tags (attributes) in feature it renders:
Name Value Description ---- ----- ----------- wigfile path name Path to the Bio::Graphics::Wiggle file or object for quantitative values. wigdata string Data exported from a Bio::Graphics::Wiggle in WIF format using its export_to_wif64() method. densefile path name Path to a Bio::Graphics::DenseFeature object (deprecated) denseoffset integer Integer offset to where the data begins in the Bio::Graphics::DenseFeature file (deprecated) densesize integer Integer size of the data in the Bio::Graphics::DenseFeature file (deprecated)
BUGSPlease report them.
AUTHORLincoln Stein <[email protected]>.
Copyright (c) 2007 Cold Spring Harbor Laboratory
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.