[Bioperl-l] Bio::Graphics : To change scale color & sort and add direction to SeqFeature

Chris Fields cjfields at uiuc.edu
Mon Aug 13 10:39:11 EDT 2007


On Aug 13, 2007, at 6:07 AM, Shameer Khadar wrote:

> Dear All,
>
> I am generating images based on Transcription Factor binding site data
> using bio::graphics module.
> I created my images using program : version-2
> [http://stein.cshl.org/genome_informatics/BioGraphics/] (Courtsey : L.
> Stein ). I attaching one of the image with this mail.
>
> I need to make 3 changes to this image
>
> 1. to color the 'scale'
> Color the scale in two different colors ie, from start 1.0k - color  
> blue
> from 101 - till end of the scale green (I thoroghly checked the
> Bio::Graphics document, I couldnt find an option to do this )

Much of the documentation you need is available via 'perldoc  
Bio::Graphics::Panel' and the various Bio::Graphics::Glyph classes.   
The above may be possible using two seqfeatures instead of one or  
maybe a split location with a callback (not sure, haven't tried  
either, mileage may vary, batteries not included, warranty void if  
packaging is opened, etc).  Might be worth checking out the POD for  
the arrow glyph to see what's possible.

> 2. to sort the Transcription factors based on the z_score

In Bio::Graphics::Panel POD under 'Glyph Options', there is  
documentation for 'sort_order' which accepts callbacks.  According to  
the docs you would basically do something like the following (the  
prototype is required; note the score):

   -sort_order => sub ($$) {
     my ($glyph1,$glyph2) = @_;
     my $a = $glyph1->feature;
     my $b = $glyph2->feature;
     ( $b->score/log($b->length)
           <=>
       $a->score/log($a->length) )
           ||
     ( $a->start <=> $b->start )
   }

Again, haven't tried.

> 3. to give forward/reverse [> or < ]direction for the black boxes

I think you first need to ensure the glyph will accept strandedness,  
though I think most do.  Then you would set either the 'strand_arrow'  
or 'stranded' option to 1 (they are synonyms).  Again, see  
Bio::Graphics::Panel POD under Glyph Options, specifically the  
parameter 'stranded' or 'strand_arrow'.

> I would appreaciate if any one can give me some clues/link to  
> accomplish
> this :).
> thanks in advance ,
> Shameer

No problem!

chris

> -- 
> Shameer Khadar
> Lab (# 25) The Computational Biology Group
> National Centre for Biological Sciences (TIFR)
> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> T - 91-080-23666001 EXT - 6251
> W - http://www.ncbs.res.in
> <TF_top3.png>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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