This article describes glyphs and glyph configuration options in GBrowse.
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.