Hi Noah,<div><br></div><div>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. </div>
<div><br></div><div>Lincoln <br><br><div class="gmail_quote">On Fri, Jun 4, 2010 at 8:04 PM, Noah Fahlgren <span dir="ltr"><<a href="mailto:fahlgren@cgrb.oregonstate.edu">fahlgren@cgrb.oregonstate.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">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:<br>
<br>
[lib127]<br>
feature = smallRNA127<br>
database = smallRNA<br>
glyph = generic<br>
key = Col-0<br>
height = 4<br>
fgcolor = \&multicolorDisplay<br>
bgcolor = \&multicolorDisplay<br>
strand_arrow = 1<br>
description = 0<br>
label = sub {<br>
my $feature = shift;<br>
my $note = $feature->score." RPM";<br>
return $note;<br>
}<br>
label_density = 50<br>
bump density = 1000<br>
category = Fahlgren et al. 2009<br>
citation = small RNA from wild type (Col-0) whole-aerial, bolting plants (Fahlgren et al. 2009).<br>
<br>
[lib127:1000]<br>
feature = smallRNA127_100<br>
database = histograms<br>
glyph = xyplot<br>
height = 50<br>
fgcolor = black<br>
bgcolor = black<br>
strand_arrow = 0<br>
description = 0<br>
label = 0<br>
group_on = display_name<br>
graph_type = boxes<br>
max_score = 100<br>
min_score = -100<br>
clip = 1<br>
part_color = \&multicolorDisplay<br>
<br>
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:<br>
<br>
Individual small RNA:<br>
Chr1 ASRP smallRNA127 75 98 1.52 - . ID=ASRP1672607;Index=0<br>
Chr1 ASRP smallRNA127 154 177 1.52 + . ID=ASRP782716;Index=0<br>
Chr1 ASRP smallRNA127 170 192 4.56 + . ID=ASRP331607;Index=0<br>
Chr1 ASRP smallRNA127 171 194 1.52 + . ID=ASRP7739156;Index=0<br>
Chr1 ASRP smallRNA127 543 566 1.52 + . ID=ASRP2341059;Index=0<br>
Chr1 ASRP smallRNA127 594 617 1.52 + . ID=ASRP3944461;Index=0<br>
Chr1 ASRP smallRNA127 752 775 1.52 + . ID=ASRP2891574;Index=0<br>
Chr1 ASRP smallRNA127 772 795 1.52 + . ID=ASRP827103;Index=0<br>
<br>
Histogram data:<br>
Chr1 ASRP smallRNA127_100 110 130 1.52 + . Name=smallRNA127_100;SizeClass=24;Index=0<br>
Chr1 ASRP smallRNA127_100 130 150 7.6 + . Name=smallRNA127_100;SizeClass=23;Index=0<br>
Chr1 ASRP smallRNA127_100 150 170 7.6 + . Name=smallRNA127_100;SizeClass=23;Index=0<br>
Chr1 ASRP smallRNA127_100 170 190 7.6 + . Name=smallRNA127_100;SizeClass=23;Index=0<br>
Chr1 ASRP smallRNA127_100 190 210 7.6 + . Name=smallRNA127_100;SizeClass=23;Index=0<br>
Chr1 ASRP smallRNA127_100 210 230 6.08 + . Name=smallRNA127_100;SizeClass=23;Index=0<br>
Chr1 ASRP smallRNA127_100 510 530 1.52 + . Name=smallRNA127_100;SizeClass=24;Index=0<br>
Chr1 ASRP smallRNA127_100 530 550 1.52 + . Name=smallRNA127_100;SizeClass=24;Index=0<br>
Chr1 ASRP smallRNA127_100 550 570 3.04 + . Name=smallRNA127_100;SizeClass=24;Index=0<br>
<br>
Am I missing something? I used to do this in Gbrowse 1.7, but maybe something has changed.<br>
<br>
Thanks,<br>
Noah<br>
<br>
-- <br><font color="#888888">
Noah Fahlgren<br>
Graduate Research Assistant<br>
Center for Genome Research and Biocomputing<br>
3021 ALS Building<br>
Oregon State University<br>
Corvallis, OR 97331<br>
Phone: 541-737-3679<br>
Email: <a href="mailto:fahlgren@cgrb.oregonstate.edu" target="_blank">fahlgren@cgrb.oregonstate.edu</a><br>
<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>
416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br>
</div>