[Bioperl-l] Re: Quick bio::graphics question

[Adam Woolfe]

In reply to this, Im also trying to get the ruler to show not 1-130000 but
from 60000-130000 when I try doing this using the following code:

	$seqlength = 130000;
	$start = 60000;
	$end = $seqlength;
	$length = $seqlength - $start;

	#create a new Panel object
	my $panel = Bio::Graphics::Panel->new(-length => $length,
                                     	      -key_style=>'between',
				     	      -width  =>1100,
                                              -pad_left => 10,
                                              -pad_right => 10,
				              -pad_top => 10,
				              -pad_bottom => 10);


	my $full_length = Bio::SeqFeature::Generic->new(-start=>$start,-end=>$seqlength);

	$panel->add_track($full_length,
      		            -glyph   => 'arrow',
               		    -tick    => 2,
               		    -fgcolor => 'black',
                	    -double  => 1,
		 	    -base => 'true');


then it doesnt work. If you try and smaller figure to start (e.g. 5000)
then it works but it just shifts the ruler to the right and draws it as it
did before but just missing out the first 5000, which is obviously no
good. I also want to give it co-ordinates as before for exon structures in
the same place but I want it to draw it in the correct place in relation
to the new ruler. Can you do this?

cheers,

Adam


Adam Woolfe
Comparative Genomics Group
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494500  Fax: +44 1223 494512
E-mail: awoolfe at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk

On Sat, 1 May 2004, Lincoln Stein wrote:

> Hi Tim,
>
> Sorry it took so long for me to respond, but I've been traveling and reading
> my e-mail intermittently.  If you create a feature that starts and stops in
> chromosomal coordinates, rather than going from 1 to $length, then the ruler
> will show the appropriate coordinates.  Simple, eh?
>
> I hope this fixes your problem.
>
> Lincoln
>
> On Thursday 22 April 2004 09:41 am, Tim Nugent wrote:
> > Hi Lincoln,
> >
> > Quick bio::graphics question. How can I get the ruler to show actual
> > chromosomal coordinates rather than 0 to the end of panel in 10K
> > increments?
> >
> > Cheers,
> >
> > Tim
> >
> > 	my $full_length = Bio::SeqFeature::Generic->new(-start=>1,
> >
> > -end=>$length);
> >
> > 	$panel->add_track($full_length,
> > 			      -glyph   => 'arrow',
> > 			      -tick    => 2,
> > 			      -fgcolor => 'black',
> > 			      -double  => 1
> > 			  );
>
> --
> Lincoln Stein
> lstein at cshl.edu
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
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