[Bioperl-l] Bio::Graphics funkiness

Jean-Jack Riethoven pow at ebi.ac.uk
Wed Jul 21 12:13:10 EDT 2004

On Wed, 21 Jul 2004, Josh Lauricha wrote:

> Where that is one track (one sequence) of type graded_segments. I would
> like them to show up on a single "line". I am guessing that the little
> black border around them is wider than the gap it is trying to show. How
> would I force them to be on the same line? The goal is to give an Idea
> of how the multiple alignment looks.

Set your bump level to 0, -bump => 0

However, you might night to devise a way to distinguish between the
separate features (aligments) then since they will connect with eachother.

You can use a code reference to give individual features different colours
(if you are not using the glyph that colour grades them by default), or
change the glyph itself if for example the individual aligment is tiny
compared to the region you want to display.

e.g. in your add_track

-glyph => sub {
		my $feature = shift;

		return ($feature->length < XX) ? "diamond" : "line";

where XX is a variable that determines when something is 'tiny' compared
to your region.

With kind regards,

Drs. Jean-Jack M. Riethoven

EMBL Outstation - Hinxton           pow at ebi.ac.uk     ICQ#: 3433929
European Bioinformatics Institute   Phone: (+44) 1223 494635      
Wellcome Trust Genome Campus        Fax  : (+44) 1223 494468
Hinxton, Cambridge CB10 1SD         URL  : http://www.ebi.ac.uk/asd/

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