Glyphs and Glyph Options


See also: GBrowse Configuration/Glyphs

GBrowse offers many different options for displaying tracks. Tracks are generated by the Perl Bio::Graphics module, which is the definitive reference for the various display options in GBrowse. This page provides an introduction to the most commonly used glyphs.

Selecting and Configuring Glyphs

Every GBrowse [Track] stanza should have a glyph option. This option selects the shape and behavior of each feature rendered in the track. Other options fine tune the glyph’s appearance by selecting its height, color, and other display properties. Several standard display options are shared among all glyphs; others are glyph-specific.

The simplest [Track] stanza will look like this:

Sample track containing 5 “stacked” wiggle_xyplot glyphs.

An xy-plot compatible with dense “wig” data. See the documentation for Bio::Graphics::Glyph::wiggle_xyplot.

It produces the typical xyplot, but uses the wig data for dense data sets. In the example the bicolor_pivot parameter has been set to 0, and the pos_color and neg_color were set to obtain the conditional coloring.

feature       = Mooney_wiggle
glyph         = wiggle_xyplot
height        = 20
fgcolor       = black
bicolor_pivot = 0
pos_color     = red
neg_color     = blue
key           = Mooney ChIP-chip (Plot)
category      = Experimental Data
label         = 0
citation      = Mooney RA, Davis SE, Peters JM, Rowland JL et al.
                Regulator trafficking on bacterial transcription units in vivo. Mol Cell 2009 Jan 16;33(1):97-108.
label         = 1