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Gmane
From: Senanu <senanu.junk <at> gmail.com>
Subject: Eliminating foreground color in Bio::Graphics
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Saturday 16th November 2013 08:08:40 UTC (over 2 years ago)
Hi all,

I am using the Bio::Graphics module to draw pictures of alignments.
However, the glyphs (both 'generic' and 'graded_segments') take up more
space than they should because the 'foreground' extends beyond the actual
coordinates. This makes it so that 2 adjacent regions appear to overlap
slightly even if the genomic coordinates indicate that they do not. Do any
of you know if its possible to eliminate the foreground? My code uses:

my $panel = Bio::Graphics::Panel->new(
 …etc...
);
 my $track = $panel->add_track(
       -glyph       => 'graded_segments',
    #   -vary_fg     => 1,
       -bgcolor     => 'blue',
       -fgcolor     => 'blue:127',
       -bump        => 1,
   );
    $track->add_feature(@features);

I have tried using "-fgcolor => 'transparent' ". Making fgcolor => 'white'
doesn't do the trick either, because then it is too narrow, I suspect
because the foreground border covers up a bit of the (desired) background.

Any pointers as to how to get the glyph exactly the right size would be
much appreciated,
Thanks in advance,
Senanu
 
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