The GMOD.org wiki is read only while we transition to a new server. If you'd like to test out the new server, you can navigate to http://wiki.scottcain.net/.

GBrowse Configuration/Glyphs

From GMOD
Revision as of 13:57, 9 July 2010 by DanBolser (Talk | contribs)

Jump to: navigation, search

This article describes glyphs and glyph configuration options in GBrowse.


Glyphs and Glyph Options

A large variety of glyphs are available, and more are being added as the Bio::Graphics module grows.

A list of the common glyphs and their options is provided by the GBrowse itself. Click on the "[Help]" link in the section labeled "Upload your own annotations". This page also lists the valid foreground and background colors. Most of the glyphs are found in the BioPerl distribution, but a few are distributed directly with GBrowse.

Predefined glyphs are:

Glyph Description
Glyph Common options for all glyphs. (Glyph is the parent class of all the glyphs).
allele_tower genotype found at a SNP position
anchored_arrow a span with vertical bases |-----|. If one or the other end of the feature is off-screen, the base will be replaced by an arrow.
arrow an arrow
box another rectangle; doesn't show subparts of features
cds shows the reading frame of spliced transcripts; used in conjunction with the "coding" aggregator (GFF2).
crossbox
diamond a point-like feature represented as a triangle
dna DNA and GC content
dot
ellipse
extending_arrow
generic a rectangle
graded_segments
heterogeneous_segments a multi-segmented feature in which each segment can have a distinctive color. For Jim Kent's WABA features, this works with the waba_alignment aggregator.
idiogram This takes specially-formatted feature data and turns it into an idiogram of a Giemsa-stained metaphase chromosome. (This is included in the GBrowse distribution, not in BioPerl.)
image this embeds photographic images and/or diagrams on features processed_transcript multi-purpose representation of a spliced mRNA, including positions of UTRs
line
primers
processed_transcript
rndrect
ruler_arrow
segments a multi-segmented feature such as an alignment
span like anchored_arrow, except that the ends are truncated at the edge of the panel, not turned into an arrow
toomany
trace reads an SCF trace file and draws a graphic representation
transcript a gene model
transcript2 a slightly different representation of a gene model
translation 1-, 3- and 6-frame translations
triangle a point-like feature represented as a diamond
wormbase_transcript yet another gene model that can show UTR segments (for features that conform to the WormBase gene schema). Used in conjunction with the "wormbase_gene" aggregator (GFF2).
wiggle_density Quantitative information from wiggle files (.wig) shown as color intensity. See GBrowse/Uploading Wiggle Tracks.
wiggle_xyplot Quantitative information from wiggle files shown as an xyplot.
xyplot histograms and line plots

A more definitive list of glyph options can be found in the Bio::Graphics manual pages. Consult the manual pages for the following modules:


The "perldoc" command is handy for reading the documentation from the Unix command line. For example:

  perldoc Bio::Graphics::Glyph::primers

This will provide you with a summary of the options that apply to the "primers" glyph.

In the manual pages, the glyph options are presented the way they are called from Perl. For example, the documentation will tell you to use the -connect_color option to set the color to use when drawing the line that connects the two inward pointing arrows in the primer pair glyph. This translates to the configuration file as an option named "connect_color". For example:

[PCR Products]
glyph = primer
connect_color = blue

When referring to colors, you can use a variety of color names such as "blue" and "green". To get the full list, cut and paste the following magic incantation into the command line:

perl -MBio::Graphics::Panel -e 'print join "\n",Bio::Graphics::Panel->color_names'

or see this URL:

 http://www.wormbase.org/db/seq/gbrowse?help=annotation

Alternatively, you can use the #RRGGBB notation to specify the red, green and blue components of the color. Refer to any book on HTML for the details on using the notation.

Facts about "GBrowse Configuration/Glyphs"RDF feed
Bp:Module:BioGlyph +, allele_tower +, anchored_arrow +, arrow +, box +, cds +, crossbox +, diamond +, dna +, dot +, ellipse +, extending_arrow +, generic +, graded_segments +, heterogeneous_segments +, image +, line +, primers +, processed_transcript +, rndrect +, ruler_arrow +, segments +, span +, toomany +, transcript +, transcript2 +, translation +, triangle + and xyplot +
Glyphallele_tower +, anchored_arrow +, arrow +, box +, cds +, crossbox +, diamond +, dna +, dot +, ellipse +, extending_arrow +, generic +, graded_segments +, heterogeneous_segments +, image +, line +, primers +, processed_transcript +, rndrect +, ruler_arrow +, segments +, span +, toomany +, transcript +, transcript2 +, translation +, triangle + and xyplot +
GraphicsGlyph +, allele_tower +, anchored_arrow +, arrow +, box +, cds +, crossbox +, diamond +, dna +, dot +, ellipse +, extending_arrow +, generic +, graded_segments +, heterogeneous_segments +, image +, line +, primers +, processed_transcript +, rndrect +, ruler_arrow +, segments +, span +, toomany +, transcript +, transcript2 +, translation +, triangle + and xyplot +