[Bioperl-l] [Gmod-gbrowse] example pictures of all the glyphs?

Lincoln Stein lincoln.stein at gmail.com
Wed Nov 12 12:29:38 EST 2008

There are a pair of scripts in bioperl which generate png images of some of
the more esoteric glyphs, but the list of glyphs is not complete, as their
names are hard-coded. Perhaps these scripts can be used as the basis for a
more general script that traverses the Bio/Graphics/Glyph subdirectory,
loads each glyph it finds, and draws it.
For what it's worth, the scripts are located here:


On the todo list is a way for glyphs to self-document their parameters. To
do this, glyphs will need to support two new methods:

 sub parameters()
     return a hashref consisting of all the options they recognize as keys,
which in turn points to a hashref containing a human readable description of
the option, and a machine-readable description of the type of data that can
be passed. Here's the concept:

    height => {description => 'height of the glyph in pixels',
               range       => 'integer(1..100)'
    fgcolor => {description => 'color of the outline of the glyph',
                range       => 'color'
    bump     => {description => 'true if features should not overlap',
                 range       => 'boolean'
    sort      => {description => 'sort order',
                  range       => '{by_name,by_score,by_position}'

This is all conceptual. In fact the range should use some sort of Perl
prototyping, such as the one used by Class::Struct.

In any case, this would let us achieve two things. One is to generate a page
illustrating glyph types, as you originally asked about. The other is to
enable sophisticated editing of gbrowse track configurations by the user.

On Wed, Nov 12, 2008 at 11:42 AM, Adam Witney <awitney at sgul.ac.uk> wrote:

> I was just wondering if there are any example pictures of all the
> available glyphs somewhere?
> thanks
> adam
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Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>

Cold Spring Harbor Laboratory
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Assistant: Sandra Michelsen <michelse at cshl.edu>

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