[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
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!
Lincoln Stein wrote:
>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:
>>I have a question about controlling the vertical position of glyphs
>>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
>>I'd appreciate any suggestions you or others on the list might
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
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