[Bioperl-l] Bio::Graphics::Panel

Crabtree, Jonathan crabtree at tigr.org
Wed Jul 21 09:45:37 EDT 2004

> When using Bio::Grahpics::Panel and Bio::SeqFeature::Generic 
> to render my BLAST hits as a PNG image, I want ALL HSP's to 
> be the same color, no matter what their score or e-value is.
> How do I do that?  I have tried setting $hsp->evalue("1E-40") 
> (arbitrary high value) but it has no effect.  Which part of 
> the HSP object does Panel use to figure out what color it 
> should draw it?  Some of my HSPs are so pale they are almost 
> invisible.

What glyph are you using to display the HSPs (i.e., what value are you
passing as the 'glyph' when you call add_track on the objects that
represent the HSPs)?  If you're currently using the 'graded_segments'
glyph, try changing it to a plain old 'segments' glyph and see what
happens; the former sets the intensity of the color based on the
features' scores, while the latter does not.


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