[Bioperl-l] Eliminating foreground color in Bio::Graphics

Senanu senanu.junk at gmail.com
Sat Nov 16 08:08:40 UTC 2013

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(
 my $track = $panel->add_track(
       -glyph       => 'graded_segments',
    #   -vary_fg     => 1,
       -bgcolor     => 'blue',
       -fgcolor     => 'blue:127',
       -bump        => 1,

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,

More information about the Bioperl-l mailing list