[Bioperl-l] xyplot glyph: scale problems

Luis A. M. Quintales lamq at usal.es
Mon Apr 14 11:01:51 EDT 2008


I have some problem with the xyplot scale numbers calculated by the glyph.

The shape of the graph looks fine, but the scale number 10 and his 
position in the ouput is not correct.

I send the source code, simplified input file and the png output.

Thank you


Source code

ex1.pl  (also in http://avellano.usal.es/~luis/bioperl-l/ex1.pl)
============================
#!/usr/bin/perl
use Bio::DB::GFF;
use Bio::Graphics::Panel;
use strict;

my $filin  = $ARGV[0];
my $db = Bio::DB::GFF->new( -dsn => $filin,-adaptor => 'memory',
                            -aggregator => 'at{atpc:atfreq}' );
my $segment  = $db->segment('chr1');
my @features = $segment->features('at');
my $panel = Bio::Graphics::Panel->new(
       -offset    => 0, -grid    => 100,                               
       -length    => 500, -width     => 800,
       -pad_left  => 50, -pad_right => 50 );
$panel->add_track($segment, -glyph   => 'generic',
                           -bgcolor => 'blue', -label   => 
1);                                    
$panel->add_track(\@features,
                    -glyph => 'xyplot',
                    -graph_type=>'boxes',
                    -scale=>'left',
                    -height=>200,
 );
open (FI,"> sal.png");
============================

in1.gff file (also in http://avellano.usal.es/~luis/bioperl-l/in1.gff)
============================
##sequence-region chr1 1 5578650
chr1    atfreq    atpc    1    10       64.0000    .    .    atpc 1
chr1    atfreq    atpc    11    20       63.0000    .    .    atpc 1
chr1    atfreq    atpc    21    30       62.0000    .    .    atpc 1
chr1    atfreq    atpc    31    40       59.0000    .    .    atpc 1
chr1    atfreq    atpc    41    50       59.0000    .    .    atpc 1
chr1    atfreq    atpc    51    60       59.0000    .    .    atpc 1
chr1    atfreq    atpc    61    70       59.0000    .    .    atpc 1
chr1    atfreq    atpc    71    80       59.0000    .    .    atpc 1
chr1    atfreq    atpc    81    90       61.0000    .    .    atpc 1
chr1    atfreq    atpc    91    100       60.0000    .    .    atpc 1
chr1    atfreq    atpc    101    110       60.0000    .    .    atpc 1
chr1    atfreq    atpc    111    120       64.0000    .    .    atpc 1
chr1    atfreq    atpc    121    130       64.0000    .    .    atpc 1
chr1    atfreq    atpc    131    140       60.0000    .    .    atpc 1
chr1    atfreq    atpc    141    150       60.0000    .    .    atpc 1
chr1    atfreq    atpc    151    160       63.0000    .    .    atpc 1
chr1    atfreq    atpc    161    170       62.0000    .    .    atpc 1
chr1    atfreq    atpc    171    180       59.0000    .    .    atpc 1
chr1    atfreq    atpc    181    190       54.0000    .    .    atpc 1
chr1    atfreq    atpc    191    200       53.0000    .    .    atpc 1
chr1    atfreq    atpc    201    210       54.0000    .    .    atpc 1
chr1    atfreq    atpc    211    220       50.0000    .    .    atpc 1
chr1    atfreq    atpc    221    230       51.0000    .    .    atpc 1
chr1    atfreq    atpc    231    240       56.0000    .    .    atpc 1
chr1    atfreq    atpc    241    250       58.0000    .    .    atpc 1
chr1    atfreq    atpc    251    260       55.0000    .    .    atpc 1
chr1    atfreq    atpc    261    270       54.0000    .    .    atpc 1
chr1    atfreq    atpc    271    280       56.0000    .    .    atpc 1
chr1    atfreq    atpc    281    290       59.0000    .    .    atpc 1
chr1    atfreq    atpc    291    300       58.0000    .    .    atpc 1
chr1    atfreq    atpc    301    310       60.0000    .    .    atpc 1
chr1    atfreq    atpc    311    320       59.0000    .    .    atpc 1
chr1    atfreq    atpc    321    330       59.0000    .    .    atpc 1
chr1    atfreq    atpc    331    340       57.0000    .    .    atpc 1
chr1    atfreq    atpc    341    350       56.0000    .    .    atpc 1
chr1    atfreq    atpc    351    360       57.0000    .    .    atpc 1
chr1    atfreq    atpc    361    370       57.0000    .    .    atpc 1
chr1    atfreq    atpc    371    380       58.0000    .    .    atpc 1
chr1    atfreq    atpc    381    390       56.0000    .    .    atpc 1
chr1    atfreq    atpc    391    400       58.0000    .    .    atpc 1
chr1    atfreq    atpc    401    410       56.0000    .    .    atpc 1
chr1    atfreq    atpc    411    420       59.0000    .    .    atpc 1
chr1    atfreq    atpc    421    430       58.0000    .    .    atpc 1
chr1    atfreq    atpc    431    440       59.0000    .    .    atpc 1
chr1    atfreq    atpc    441    450       58.0000    .    .    atpc 1
chr1    atfreq    atpc    451    460       58.0000    .    .    atpc 1
chr1    atfreq    atpc    461    470       56.0000    .    .    atpc 1
chr1    atfreq    atpc    471    480       57.0000    .    .    atpc 1
chr1    atfreq    atpc    481    490       59.0000    .    .    atpc 1
============================


The sal.png :
http://avellano.usal.es/~luis/bioperl-l/sal.png

Thank you.


-- 
==================================================
 Luis Antonio Miguel Quintales
 Departamento de Informática y Automática
 Facultad de Ciencias
 Universidad de Salamanca
 Plaza de la Merced s/n
 37008-SALAMANCA
 SPAIN
==================================================
 Tel.: +34-923-294400(ext.1513)
 Fax.: +34-923-294584
 E-mail: lamq at usal.es
==================================================



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