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

Lincoln Stein lstein at cshl.edu
Thu Mar 1 16:23:49 EST 2007


I'm glad you picked that up. I would have never noticed the missing comma.

NB: if you set "use warnings" at the top of your script, then you would have
gotten an error message about subtraction with an undefined variable.

Lincoln

On 3/1/07, michael watson (IAH-C) <michael.watson at bbsrc.ac.uk> wrote:
>
>  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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>
>
> --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
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>



-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu


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