[Bioperl-l] [Gmod-gbrowse] aggregators issue?

Lincoln Stein lincoln.stein at gmail.com
Sun Nov 19 12:22:25 EST 2006


Hi,

What you want to do is what the heterogeneous_segments glyph does. The
redgreen_box glyph originally only operated on the top level feature and not
with aggregated features. However, since what you want to do is reasonable
I've added a new color_subparts option, so that you will get the right
effect with this modified stanza:

[Linkage2]
feature        = qtl
color_subparts = 1
glyph          = redgreen_box
key            = Linkage2

You'll need to update bioperl to get this fix.

The xyplot issue that you reported was a real bug in bioperl. This has now
been fixed in both the release candidate and HEAD CVS repositories.

Lincoln

On 11/16/06, mmorley <mmorley at mail.med.upenn.edu> wrote:
>
> Hello All,
>
> Not sure where the problem lies but I'm trying to display results from a
> Linkage analysis (many really)..
> Perhaps my logic on the data structure is wrong but I have a peak
> (locus,QTL,etc) that exceeds some defined significance that I have
> predefined.
> Within each peak there are markers (SNPs in this case) each with a level
> of significance(score). Instead of displaying each SNP value as say in
> XY plot... I have a score for the SNP to SNP interval.. The idea being
> is I'd like to display the data using the redgreen_box glyph.
>
> To make it easier I created a little small test set which can be placed
> on the Volvox tutorial ctgA
>
> Here is the gff data:
> ----------------------------------------
> ctgA    test    peak    0    40000    .    .    .    peak 3 ; Note
> "EIF4G2"
> ctgA    test    signal    0    1    0.4    .    .    peak 3 ;
> ctgA    test    signal    2    25000    0.7    .    .    peak 3 ;
> ctgA    test    signal    25000    35000    0.6    .    .    peak 3 ;
> ctgA    test    signal    35000    40000    0.5    .    .    peak 3 ;
> ctgA    test    peak    0    40000    .    .    .    peak 10 ; Note "LRAP"
> ctgA    test    signal    0    1    0.3    .    .    peak 10 ;
> ctgA    test    signal    2    25000    0.4    .    .    peak 10 ;
> ctgA    test    signal    25000    35000    0.7    .    .    peak 10 ;
> ctgA    test    signal    35000    40000    0.5    .    .    peak 10 ;
> ---------------------------------------------------
>
> here is my aggregator:
> --------------------------------------
> qtl{signal/peak}
> -----------------------------------------
> and my track:
> ---------------------------------------------
> [Linkage2]
> feature        = qtl
> glyph          = redgreen_box
> key            = Linkage2
> -------------------------------------------
>
> right now very basic... the problem is well nothing is displayed using
> that track... I do however get the label for each printed.. but no
> graphic. If I change the feature to "signal" I do get data plotted but
> each signal is on a different line,which is expected but not what I want.
>
> Also as a side note if I decide to plot the data as an xy_plot using the
> following track stanza:
> [Linkage]
> feature        = qtl
> glyph          = xyplot
> graph_type     = line
> height         = 50
> min_score      = 0
> max_score      = 1
> scale          = right
> key            = Linkage
>
> I get both peaks plotted but within the same plot... However a second
> plot is created it is just empty.
>
> Hopefully I'm convening this well... and if not hopefully fairly easy to
> test...
>
>
>        -Mike
>
>
> --
> Michael Morley
> Bioinformatics Specialist
> University of Pennsylvania
> Department of Pediatrics
> 3516 Civic Center Blvd.,
> 510B Abramson Pediatric Research Center,
> Philadelphia, PA 19104-4318.
> Phone: (215) 590-7673
> FAX: (215) 590-3709
>
>
>
>
>
>
>
>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
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(516) 367-8389 (fax)
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PLEASE CONTACT MY ASSISTANT,
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