<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
Hi Lincoln,<br>
<br>
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.<br>
<br>
Noah<br>
<br>
On 6/15/10 12:19 PM, Lincoln Stein wrote:
<blockquote
cite="mid:AANLkTim11DKdA82MtLf-Gs5nXSbw4Bdw17OuofvLn8ox@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
href="mailto:fahlgren@cgrb.oregonstate.edu">fahlgren@cgrb.oregonstate.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; 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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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: <a class="moz-txt-link-abbreviated" href="mailto:fahlgren@cgrb.oregonstate.edu">fahlgren@cgrb.oregonstate.edu</a>
</pre>
</body>
</html>