[Bioperl-l] Controlling glyph position with Bio::Graphics::Panel

Donald G. Jackson donald.jackson at bms.com
Mon Jan 5 08:45:26 EST 2004

Hi Lincoln,

I'm not sure if that's what I want or not, because I'm not exactly sure 
what a glyph is ;).

I give Bio::Graphics::Glyph::segments  a listref of all the HSPs for a 
BLAST hit and have it draw out the individual HSPs with a connector 
(I've attached an example image from my current script).  Multiple HSPs 
for the same hit are connected by dashed lines;  in other cases there 
are hsps from different hits close to each other - most users would 
think these were also from the same hit.

If the set of connected HSPs is a single  glyph, then it sounds like 
your old code would do the trick.  If each individual HSP is a glyph 
then that wouldn't work.  If it's easy to dig out an older version of 
the code with the -bump=>2 option I'd like to give it a try and see what 

I agree that most of the time the bump=>1 behavior makes the most sense, 
but for search results I think it's confusing - the 1 track = 1 hit is 
easier for people to keep straight.

Thanks very much for your help!

Don Jackson

Lincoln Stein wrote:

>Hi Don,
>There used to be a -bump=>2 option, which turned on the kind of 
>bumping that (I think) you want.  No two glyphs are allowed to occupy 
>the same Y position in the track.  This option was removed when I 
>found a way to speed up the regular bumping; I never really liked it.
>I can go back in CVS time and try to resurrect -bump=>2, but please 
>confirm that this is what you're looking for.
>On Friday 02 January 2004 11:23 am, Donald Jackson wrote:
>>Hi Lincoln,
>>I have a question about controlling the vertical position of glyphs
>>using Bio::Graphics::Panel.
>>I'm drawing out hits and hsps from a blast search (as lists of
>>Bio::Search::HSP objects) using the segments glyph.  I've run into
>>a problem when I have two non-overlapping hits.  I'd like to force
>>these to appear at distinct y-coordinates in the image, but can't
>>figure out how to do this.  I tried 'bump', but that only affects
>>_overlapping_ hits.
>>I'd appreciate any suggestions you or others on the list might
>>Don Jackson
>>BMS Bioinformatics
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org

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