[Bioperl-l] Can Bio::Graphics render a muti_segments picture?

[Lincoln Stein]

Hi,

I highly recommend using version 1.2 for a whole host of reasons. Try 1.2, and 
if the GC plot still isn't working, let me know. 

Lincoln

On Wednesday 14 May 2003 05:23 am, tongw wrote:
> Hi, Lincoln,
>         I met the same problem emerged in the mail of Lucas Quincy Ton
> in Feb 3,2003:
>         "Using the 'dna' glyph of Bio::Graphics  to render GC-content
> plot, I get the plot but with just
> a straight line in the middle (50%) from lelf to right".  And you
> answered, "I have checked in a new version of the dna.pm module that
> should fix this so that the GC content glyph will work
> correctly".
>         So I want to know whether the problem in dna glyph has been
> fixed in bioperl version 1.2.
>
>
> Wei Tong
>
>
> -----Original Message-----
> From: Lincoln Stein [mailto:lstein at cshl.org]
> Sent: 2003Äê5ÔÂ14ÈÕ 05:41
> To: tongw
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Can Bio::Graphics render a muti_segments
> picture?
>
>
> Hi Wei,
>
> If you are trying to wrap the picture so that it spans multiple lines,
> like a
> paragraph of text, then Bio::Graphics won't do that automatically.  The
> best
> that you can do is to generate one very long GD image, and then to break
> it
> into small rectangles and paste them back together into the desired
> geometry
> using the $gd->copy() function.
>
> Lincoln
>
> On Monday 12 May 2003 11:00 pm, tongw wrote:
> > Hi, dear Lincoln:
> >        Thanks for your so quick response. It`s the problem of my
> > English expression about my previous question. My puzzle is:
> >     When your sequence is too long to be drawn in one line, can
> > Bio::Graphics help us to draw the long sequence in muti_parts, such as
> >
> > drawing a 200k sequence in two parts, each is 100k. But not to say how
> >
> > to draw  a muti_segments feature in a sequence.
> >        Because I want to write a script to draw the picture of genes`
> > annotation of small genomes by the Bio::Graphics module, which are too
> >
> > long to display in one line. Kind Regards.
> >                                                     Wei Tong
> >
> >
> > -----Original Message-----
> > From: Lincoln Stein [mailto:lstein at cshl.org]
> > Sent: 2003Äê5ÔÂ12ÈÕ 21:54
> > To: tongw; bioperl-l at bioperl.org
> > Subject: Re: [Bioperl-l] Can Bio::Graphics render a muti_segments
> > picture?
> >
> >
> > Here's an example of drawing a multi-segment object:
> >
> > use strict;
> > use Bio::Graphics;
> > use Bio::SeqFeature::Generic;
> >
> > my $Generic = 'Bio::SeqFeature::Generic';  # to reduce typing
> >
> > # create a feature to use for the scale arrow
> > my $whole_region = $Generic->new(-start=>1,
> > -end=>10000,-seq_id=>'whole');
> >
> > # create a multi-segment feature
> > my $blue1        =
> > $Generic->new(-start=>5000,-end=>9000,-seq_id=>'blue1');
> > $blue1->add_SeqFeature($Generic->new(-start=>5000,-end=>6000));
> > $blue1->add_SeqFeature($Generic->new(-start=>7000,-end=>7500));
> > $blue1->add_SeqFeature($Generic->new(-start=>8000,-end=>9000));
> >
> > my $panel =
> > Bio::Graphics::Panel->new(-segment=>$whole_region,-width=>800);
> > $panel->add_track($whole_region,
> >                   -glyph  => 'arrow',
> >                   -double => 1,
> >                   -tick   => 2);
> >
> > $panel->add_track($blue1,
> >                   -glyph   => 'segments',
> >                   -label   => 1,
> >                   -bgcolor => 'blue');
> >
> > print $panel->png;
> >
> > Best,
> >
> > Lincoln
> >
> > On Monday 12 May 2003 06:18 am, tongw wrote:
> > > Greeting all, especially the developers of Bioperl:
> > >     It`s my first time to locate the mail list of Bioperl, and I
> > > have applied the Bioperl modules to sovle the problems in my
> > > research, which is more comfotable than write the perl scripts,
> > > specially in the
> > >
> > > format changing and drawing the picture by GD module.
> > >   But I meet a question: I think the Bio::Graphics only draw the
> > > whole
> > >
> > > sequence in one segment. I want to know whether there is some
> > > methods to render a muti_segments picture, and it is more necessary
> > > when the sequence is very long. Kind Regards. Specially thank
> > > Lincoln, your howto docment about Graphics helps me to grasp the
> > > main usages in graphics module.
> > >
> > >                                                        Wei Tong
> > >
> > >
> > > ============================================
> > >
> > > Wei Tong
> > >
> > > Bioinformatics Department
> > > Beijing Genomics Institute/
> > > Genomics & Bioinformatics Center Chinese Academy of Science Beijing
> > > Airport Industrial Zone B6 Beijing 101300, P.R. China
> > >
> > > Tel: 0086-10-80481833 (Office)
> > > Email : tongw at genomics.org.cn
> > > http://www.genomics.org.cn
> > > ============================================
> > >
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at bioperl.org
> > > http://pw600a.bioperl.org/mailman/listinfo/bioperl-l

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================