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

Sendu Bala bix at sendu.me.uk
Mon Aug 13 13:11:50 UTC 2007

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 )

The scale is just a scale and shouldn't need colouring. You can do what 
you want by having a blue 'upstream' feature and a green 'gene' feature 
in the first row.

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

I don't know Bio::Graphics well enough, but am interested in the answer...

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

Presumably you just change the glyph type of your binding sites to 
something that shows direction, like 'processed_transcript'. Someone 
else may have a more appropriate suggestion.

However, do your binding sites really have a direction? That is, do you 
really know which strand your transcription factor bound to?

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