[Gmod-help] Gbrowse2 semantic feature switching

[Noah Fahlgren]

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