[Gmod-help] Gbrowse2 semantic feature switching

[Noah Fahlgren]

Hi Lincoln,

That is correct, the histogram works when it is the primary stanza, but 
not the semantically zoomed stanza. I applied the patch and now it works 
great. Thanks so much for your help.

Noah

On 6/15/10 12:19 PM, Lincoln Stein wrote:
> Hi Noah,
>
> Please confirm: the histogram is working correctly when you make it 
> the primary stanza instead of the semantically zoomed stanza? I think 
> I know what the problem is. If you can, please try patching 
> Bio/Graphics/Browser2/RenderPanels.pm with the enclosed patch file. I 
> am 90% sure it will fix the problem.
>
> Lincoln
>
> On Fri, Jun 4, 2010 at 8:04 PM, Noah Fahlgren 
> <fahlgren at cgrb.oregonstate.edu <mailto:fahlgren at cgrb.oregonstate.edu>> 
> wrote:
>
>     I have a database populated with sequenced small RNA and I am
>     trying to create a track that displays the individual sequences
>     below 1,000 nts and displays histogram density data with scrolling
>     windows above.  Here is my track configuration:
>
>     [lib127]
>     feature         = smallRNA127
>     database        = smallRNA
>     glyph           = generic
>     key             = Col-0
>     height          = 4
>     fgcolor         = \&multicolorDisplay
>     bgcolor         = \&multicolorDisplay
>     strand_arrow    = 1
>     description     = 0
>     label           = sub {
>                            my $feature = shift;
>                            my $note = $feature->score." RPM";
>                            return $note;
>                    }
>     label_density   = 50
>     bump density    = 1000
>     category        = Fahlgren et al. 2009
>     citation        = small RNA from wild type (Col-0) whole-aerial,
>     bolting plants (Fahlgren et al. 2009).
>
>     [lib127:1000]
>     feature         = smallRNA127_100
>     database        = histograms
>     glyph           = xyplot
>     height          = 50
>     fgcolor         = black
>     bgcolor         = black
>     strand_arrow    = 0
>     description     = 0
>     label           = 0
>     group_on        = display_name
>     graph_type      = boxes
>     max_score       = 100
>     min_score       = -100
>     clip            = 1
>     part_color      = \&multicolorDisplay
>
>     When I zoom out to 1,000 nts or more I get individual xyplot
>     graphs for each datapoint instead of a continuous graph. If I make
>     the xyplot stanza the default feature then I get normal xyplots.
>     Here is a sample of what I loaded into our Bio::DB::SeqFeature
>     MySQL database:
>
>     Individual small RNA:
>     Chr1    ASRP    smallRNA127    75    98    1.52    -    .  
>      ID=ASRP1672607;Index=0
>     Chr1    ASRP    smallRNA127    154    177    1.52    +    .  
>      ID=ASRP782716;Index=0
>     Chr1    ASRP    smallRNA127    170    192    4.56    +    .  
>      ID=ASRP331607;Index=0
>     Chr1    ASRP    smallRNA127    171    194    1.52    +    .  
>      ID=ASRP7739156;Index=0
>     Chr1    ASRP    smallRNA127    543    566    1.52    +    .  
>      ID=ASRP2341059;Index=0
>     Chr1    ASRP    smallRNA127    594    617    1.52    +    .  
>      ID=ASRP3944461;Index=0
>     Chr1    ASRP    smallRNA127    752    775    1.52    +    .  
>      ID=ASRP2891574;Index=0
>     Chr1    ASRP    smallRNA127    772    795    1.52    +    .  
>      ID=ASRP827103;Index=0
>
>     Histogram data:
>     Chr1    ASRP    smallRNA127_100    110    130    1.52    +    .  
>      Name=smallRNA127_100;SizeClass=24;Index=0
>     Chr1    ASRP    smallRNA127_100    130    150    7.6    +    .  
>      Name=smallRNA127_100;SizeClass=23;Index=0
>     Chr1    ASRP    smallRNA127_100    150    170    7.6    +    .  
>      Name=smallRNA127_100;SizeClass=23;Index=0
>     Chr1    ASRP    smallRNA127_100    170    190    7.6    +    .  
>      Name=smallRNA127_100;SizeClass=23;Index=0
>     Chr1    ASRP    smallRNA127_100    190    210    7.6    +    .  
>      Name=smallRNA127_100;SizeClass=23;Index=0
>     Chr1    ASRP    smallRNA127_100    210    230    6.08    +    .  
>      Name=smallRNA127_100;SizeClass=23;Index=0
>     Chr1    ASRP    smallRNA127_100    510    530    1.52    +    .  
>      Name=smallRNA127_100;SizeClass=24;Index=0
>     Chr1    ASRP    smallRNA127_100    530    550    1.52    +    .  
>      Name=smallRNA127_100;SizeClass=24;Index=0
>     Chr1    ASRP    smallRNA127_100    550    570    3.04    +    .  
>      Name=smallRNA127_100;SizeClass=24;Index=0
>
>     Am I missing something?  I used to do this in Gbrowse 1.7, but
>     maybe something has changed.
>
>     Thanks,
>     Noah
>
>     -- 
>     Noah Fahlgren
>     Graduate Research Assistant
>     Center for Genome Research and Biocomputing
>     3021 ALS Building
>     Oregon State University
>     Corvallis, OR 97331
>     Phone: 541-737-3679
>     Email: fahlgren at cgrb.oregonstate.edu
>     <mailto:fahlgren at cgrb.oregonstate.edu>
>
>
>
>
> -- 
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca 
> <mailto:Renata.Musa at oicr.on.ca>>

-- 
Noah Fahlgren
Graduate Research Assistant
Center for Genome Research and Biocomputing
3021 ALS Building
Oregon State University
Corvallis, OR 97331
Phone: 541-737-3679
Email: fahlgren at cgrb.oregonstate.edu

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