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

Shameer Khadar shameer at ncbs.res.in
Mon Aug 13 14:47:35 UTC 2007

Dear Sendu,

Thanks for your reply.

>> 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.
Thanks for the point : 'The scale is just a scale...'.
But my idea is to differentiate the scale in to three to diffentiate
between 100bp upstream region, UTR and gene start site. starting point of
scale till 0k is the 100bp upstream. From 0k till end of the current_scale
is UTR, from the end of scale gene starts, since this is a bit tough to
distinguish, we thought of this coloring option. Addition of an extra
track may is an alternate option (I tried to convince our experimental
team by adding an extra track, but they want it this way :(..)

>> 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...
It is possible, but sort_order option is available. I tried it a couple of
times but it is not  working.

>> 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.
Thanks, I will look in to it.

> However, do your binding sites really have a direction? That is, do you
> really know which strand your transcription factor bound to?
Yes, these info we collated from various experimental datasets.

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

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