[Bioperl-l] The axis of GC content in Bio::Graphics::glyph:dna

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Thu Mar 1 06:01:39 EST 2007


On further inspection, the lack of a comma was causing my karma upset -
apologies.
 
Mick

________________________________

From: michael watson (IAH-C) 
Sent: 01 March 2007 10:58
To: 'lincoln.stein at gmail.com'
Cc: BioPerl-List
Subject: RE: [Bioperl-l] The axis of GC content in
Bio::Graphics::glyph:dna


In fact, those pad_left and pad_right arguments have no effect
whatsoever (using bioperl 1.5.2_100)
 
 my $panel = Bio::Graphics::Panel->new(-key_style => between,
     -offset    => $start,
     -length    => $stop - $start + 1,
     -width     => 800
     -pad_left =>5000,
     -pad_right =>5000
     );

Even if I set them to 5000, the image looks exactly as if I had not set
them.
 
The only way I can get around this is to edit Glyph/dna.pm lines 184 and
186 such that $x2+3 is changed to $x2-20 - then the axes are drawn on
the image instead of outside of it.   This is obviously a hack, which
upsets my karma.
 
Mick

________________________________

From: lincoln.stein at gmail.com [mailto:lincoln.stein at gmail.com] On Behalf
Of Lincoln Stein
Sent: 15 February 2007 18:53
To: michael watson (IAH-C)
Cc: BioPerl-List
Subject: Re: [Bioperl-l] The axis of GC content in
Bio::Graphics::glyph:dna


Hi Michael,

When you set up the panel, do this:

 Bio::Graphics::Panel->new(-blah -blah,
                                         -pad_left => 20,
                                          -pad_right => 20); 

This will leave enough room on the left and right for you to see the Y
axis. Otherwise it runs off the edge of the image (ok, this is a
mis-design, but it was the only way to solve a chicken-and-egg problem
about who gets to say how wide the panel is) 

Lincoln


On 2/15/07, michael watson (IAH-C) <michael.watson at bbsrc.ac.uk> wrote: 

	Hi
	
	OK I have some great images out of this glyph, but I can't see
the axis,
	and nor is it labelled (ie does it go from 0 - 100%?) so isn't
great for
	publication.  The docs say:
	
	"NOTE: -gc_window=>'auto' gives nice results and is recommended
for 
	drawing GC content. The GC content axes draw slightly outside
the
	panel, so you may wish to add some extra padding on the right
and
	left. "
	
	Any idea how to do this?
	
	Basically, I want a nice GC graph with the axis quite clearly
labelled, 
	and a nice "%GC" title next to it :)
	
	Thanks
	
	Mick
	
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