[Bioperl-l] Bio::Graphics : To change scale color & sort and add direction to SeqFeature
bix at sendu.me.uk
Mon Aug 13 09:11:50 EDT 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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