[Bioperl-l] Can Bio::Graphics render a muti_segments picture?
tongw
tongw at genomics.org.cn
Thu May 15 10:07:25 EDT 2003
Yes, I still met some problems of rendering gc content by bioperl 1.2, I
got the plot but with just a straight line in the middle (50%) from lelf
to righ. And I can`t find more manual for the dna glyph. The following
is the code:
use strict;
use Bio::Graphics;
use Bio::SeqIO;
......
my $io = Bio::SeqIO->new(-format=>"$format" , -file=>$file) or
die("can`t open the $file.\n");
my $seq = $io->next_seq or die USAGE;
my $wholeseq =
Bio::SeqFeature::Generic->new(-start=>1,-end=>$seq->length,-seq_id=>$seq
->display_name);
$wholeseq->attach_seq($seq);
my $panel = Bio::Graphics::Panel->new(
-length => $seq->length,
-key_style => 'between',
-width => 700,
-pad_top => 30,
-pad_bottom => 30,
-pad_left => 50,
-pad_right => 50,
);
$panel->add_track($wholeseq,
-glyph => 'dna',
-fgcolor => 'black',
-height => 100,
-bgcolor => 'red',
-do_gc => 'true',
-gc_bins => 100,
-axis_color=> 'blue',
-strand => 'forward',);
......
I want to know the correct usage of dna glyph in bioperl 1.2.
Kind Regards.
Wei Tong
-----Original Message-----
From: Lincoln Stein [mailto:lstein at cshl.org]
Sent: 2003Äê5ÔÂ15ÈÕ 05:44
To: tongw
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Can Bio::Graphics render a muti_segments
picture?
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
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