aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
authorZachary Sloan2012-10-30 17:47:13 -0500
committerZachary Sloan2012-10-30 17:47:13 -0500
commitdbda821555f2e9293d824b7c3662d251c0004252 (patch)
tree603aad3dac40abb0f817e459f70d37f856fb7fb8 /wqflask
parent4353a903c4661f5c12c4d653044122cf59ef373a (diff)
downloadgenenetwork2-dbda821555f2e9293d824b7c3662d251c0004252.tar.gz
Did some work converting show_trait.html to using bootstrap for styling
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/templates/show_trait.html2558
1 files changed, 1302 insertions, 1256 deletions
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index d48f9487..ab662a77 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -1,1380 +1,1426 @@
+{% extends "base.html" %}
+{% block title %}Trait Data and Analysis{% endblock %}
+{% block content %} <!-- Start of body -->
+
+ <header class="jumbotron subhead" id="overview">
+ <div class="container">
+ <h1>{{ this_trait.symbol}}</h1>
+ <p class="lead">
+ {{ this_trait.name }}: {{ this_trait.description_fmt }}
+ </p>
+ </div>
+ </header>
+
+
+
+ <div class="container">
+ <div class="page-header">
+ <h1>{{ this_trait.species.capitalize() }} -
+ {{ fd.RISet }} -
+ {{ this_trait.symbol }}
+
+ </h1>
+ </div>
+
+ <dl class="dl-horizontal">
+ <dt>Aliases</dt>
+ <dd>{{ this_trait.alias_fmt }}</dd>
+
+ <dt>Location</dt>
+ <dd>{{ this_trait.location_fmt }}</dd>
+
+ <dt>Database</dt>
+ <dd>
+ <a href="{{ this_trait.database.url }}" target="_blank">
+ {{ this_trait.database.name }}
+ </a>
+ </dd>
+
+ <dt>
+ <a href="/blatInfo.html" target="_blank"
+ title="Values higher than 2 for the specificity are good">
+ BLAT Specifity
+ </a>
+ </dt>
+ <dd>{{ "%.1f" % (this_trait.probe_set_specificity) }}</dd>
+
+ <dt>BLAT Score</dt>
+ <dd>{{ "%i" % (this_trait.probe_set_blat_score) }}</dd>
+ </dl>
+
+ <tr>
+ <td bgcolor="#EEEEEE" class="solidBorder">
+ <table width="100%" cellspacing="0" cellpadding="5">
+ <tr>
+ <td valign="top" width="100%" bgcolor="#FAFAFA">
+ <form method="post" action="/corr_compute" name="dataInput" id="trait_data_form">
+ {# <input type="hidden" name="isSE" value="yes">
+ <input type="hidden" name="permCheck">
+ <input type="hidden" name="otherStrainVals" value="_">
+ <input type="hidden" name="FormID" value="dataEditing">
+ <input type="hidden" name="normalPlotTitle" value="Sall3: 1441186_at">
+ <input type="hidden" name="sampleVars" value="_">
+ <input type="hidden" name="additiveCheck" value="ON">
+ <input type="hidden" name="incparentsf1" value="ON">
+ <input type="hidden" name="sampleNames" value="_">
+ <input type="hidden" name="submitID" value="">
+ <input type="hidden" name="scale" value="physic">
+ <input type="hidden" name="intervalAnalystCheck" value="ON">
+ <input type="hidden" name="topten" value="">
+ <input type="hidden" name="parentsf14regression" value="OFF">
+ <input type="hidden" name="identification" value="Hippocampus M430v2 BXD 06/06 PDNN : 1441186_at">
+ <input type="hidden" name="mappingMethodId" value="1">
+ <input type="hidden" name="criteria">
+ <input type="hidden" name="other_extra_attributes" is it value="_">
+ <input type="hidden" name="otherStrainNames" value="_">
+ <input type="hidden" name="method">
+ <input type="hidden" name="showGenes" value="ON">
+ <input type="hidden" name="attribute_names" value="">
+ <input type="hidden" name="chromosomes" value="-1">
+ <input type="hidden" name="allsamplelist" value="B6D2F1 D2B6F1 C57BL/6J DBA/2J BXD1 BXD2 BXD5 BXD6 BXD8 BXD9 BXD11 BXD12 BXD13 BXD14 BXD15 BXD16 BXD18 BXD19 BXD20 BXD21 BXD22 BXD23 BXD24a BXD24 BXD25 BXD27 BXD28 BXD29 BXD30 BXD31 BXD32 BXD33 BXD34 BXD35 BXD36 BXD37 BXD38 BXD39 BXD40 BXD41 BXD42 BXD43 BXD44 BXD45 BXD48 BXD49 BXD50 BXD51 BXD52 BXD53 BXD54 BXD55 BXD56 BXD59 BXD60 BXD61 BXD62 BXD63 BXD64 BXD65 BXD66 BXD67 BXD68 BXD69 BXD70 BXD71 BXD72 BXD73 BXD74 BXD75 BXD76 BXD77 BXD78 BXD79 BXD80 BXD81 BXD83 BXD84 BXD85 BXD86 BXD87 BXD88 BXD89 BXD90 BXD91 BXD92 BXD93 BXD94 BXD95 BXD96 BXD97 BXD98 BXD99 BXD100 BXD101 BXD102 BXD103 BALB/cByJ PWK/PhJ A/J KK/HlJ LG/J 129S1/SvImJ NZO/HlLtJ CAST/EiJ PWD/PhJ AKR/J CXB13 CXB12 CXB11 CXB10 WSB/EiJ C3H/HeJ CXB7 CXB6 CXB5 CXB4 CXB3 CXB2 CXB1 CXB9 CXB8 NOD/ShiLtJ C57BL/6ByJ BALB/cJ">
+ <input type="hidden" name="applyVarianceSE">
+ <input type="hidden" name="MDPChoice">
+ <input type="hidden" name="otherStrainVars" value="_">
+ <input type="hidden" name="sampleVals" value="_">
+ <input type="hidden" name="showSNP" value="ON">
+ <input type="hidden" name="bootCheck">
+ <input type="hidden" name="GeneId" value="20689">
+ <input type="hidden" name="extra_attributes" value="_">
+ <input type="hidden" name="stats_method" value="1">
+ <input type="hidden" name="heritability" value="None">
+ <input type="hidden" name="database" value="">
+ <input type="hidden" name="viewLegend" value="ON">
+ <input type="hidden" name="fromDataEditingPage" value="1">
+ <input type="hidden" name="trait_type" value="ProbeSet">
+ <input type="hidden" name="valsHidden" value="OFF">
+ <input type="hidden" name="fullname" value="HC_M2_0606_P::1441186_at">
+ <input type="hidden" name="RISet" value="BXD">
+ #}
+ {% for key in hddn %}
+ <input type="hidden" name="{{ key }}" value="{{ hddn[key] }}">
+ {% endfor %}
+ <div>
+ <div style="font-size:14px;">
+ <strong style="font-size:16px;">Trait Data and Analysis&nbsp;</strong> for Record ID 1441186_at
+ </div>
+ </div>
+
+ <p class="sectionheader" id="title1" style="border-radius: 5px;">&nbsp;&nbsp;Details and Links</p>
+
+ <p id="sectionbody1"></p>
+
+ <table class="collap" id="target1" style="margin-left:20px;" cellpadding="2" width="840" valign="top">
+ <tr>
+ <td class="fwb fs13" nowrap="on" valign="top" width="90">Gene Symbol:</td>
+
+ <td valign="top" width="10"></td>
+
+ <td valign="top" width="740"><span class="fs13 fsI">{{ this_trait.symbol }}</span></td>
+ </tr>
+
+ <tr>
+ <td class="fwb fs13" nowrap="on" valign="top">Aliases:</td>
+
+ <td valign="top" width="10"></td>
+
+ <td valign="top"><span class="fs13 fsI">{{ this_trait.alias_fmt }}</span></td>
+ </tr>
+
+ <tr>
+ <td class="fwb fs13" nowrap="on" valign="top">Description:</td>
+
+ <td valign="top" width="10"></td>
- {% extends "base.html" %}
- {% block title %}Trait Data and Analysis{% endblock %}
- {% block content %} <!-- Start of body -->
-
- <tr>
- <td bgcolor="#EEEEEE" class="solidBorder">
- <table width="100%" cellspacing="0" cellpadding="5">
- <tr>
- <td valign="top" width="100%" bgcolor="#FAFAFA">
- <form method="post" action="/corr_compute" name="dataInput" id="trait_data_form">
- {# <input type="hidden" name="isSE" value="yes">
- <input type="hidden" name="permCheck">
- <input type="hidden" name="otherStrainVals" value="_">
- <input type="hidden" name="FormID" value="dataEditing">
- <input type="hidden" name="normalPlotTitle" value="Sall3: 1441186_at">
- <input type="hidden" name="sampleVars" value="_">
- <input type="hidden" name="additiveCheck" value="ON">
- <input type="hidden" name="incparentsf1" value="ON">
- <input type="hidden" name="sampleNames" value="_">
- <input type="hidden" name="submitID" value="">
- <input type="hidden" name="scale" value="physic">
- <input type="hidden" name="intervalAnalystCheck" value="ON">
- <input type="hidden" name="topten" value="">
- <input type="hidden" name="parentsf14regression" value="OFF">
- <input type="hidden" name="identification" value="Hippocampus M430v2 BXD 06/06 PDNN : 1441186_at">
- <input type="hidden" name="mappingMethodId" value="1">
- <input type="hidden" name="criteria">
- <input type="hidden" name="other_extra_attributes" is it value="_">
- <input type="hidden" name="otherStrainNames" value="_">
- <input type="hidden" name="method">
- <input type="hidden" name="showGenes" value="ON">
- <input type="hidden" name="attribute_names" value="">
- <input type="hidden" name="chromosomes" value="-1">
- <input type="hidden" name="allsamplelist" value="B6D2F1 D2B6F1 C57BL/6J DBA/2J BXD1 BXD2 BXD5 BXD6 BXD8 BXD9 BXD11 BXD12 BXD13 BXD14 BXD15 BXD16 BXD18 BXD19 BXD20 BXD21 BXD22 BXD23 BXD24a BXD24 BXD25 BXD27 BXD28 BXD29 BXD30 BXD31 BXD32 BXD33 BXD34 BXD35 BXD36 BXD37 BXD38 BXD39 BXD40 BXD41 BXD42 BXD43 BXD44 BXD45 BXD48 BXD49 BXD50 BXD51 BXD52 BXD53 BXD54 BXD55 BXD56 BXD59 BXD60 BXD61 BXD62 BXD63 BXD64 BXD65 BXD66 BXD67 BXD68 BXD69 BXD70 BXD71 BXD72 BXD73 BXD74 BXD75 BXD76 BXD77 BXD78 BXD79 BXD80 BXD81 BXD83 BXD84 BXD85 BXD86 BXD87 BXD88 BXD89 BXD90 BXD91 BXD92 BXD93 BXD94 BXD95 BXD96 BXD97 BXD98 BXD99 BXD100 BXD101 BXD102 BXD103 BALB/cByJ PWK/PhJ A/J KK/HlJ LG/J 129S1/SvImJ NZO/HlLtJ CAST/EiJ PWD/PhJ AKR/J CXB13 CXB12 CXB11 CXB10 WSB/EiJ C3H/HeJ CXB7 CXB6 CXB5 CXB4 CXB3 CXB2 CXB1 CXB9 CXB8 NOD/ShiLtJ C57BL/6ByJ BALB/cJ">
- <input type="hidden" name="applyVarianceSE">
- <input type="hidden" name="MDPChoice">
- <input type="hidden" name="otherStrainVars" value="_">
- <input type="hidden" name="sampleVals" value="_">
- <input type="hidden" name="showSNP" value="ON">
- <input type="hidden" name="bootCheck">
- <input type="hidden" name="GeneId" value="20689">
- <input type="hidden" name="extra_attributes" value="_">
- <input type="hidden" name="stats_method" value="1">
- <input type="hidden" name="heritability" value="None">
- <input type="hidden" name="database" value="">
- <input type="hidden" name="viewLegend" value="ON">
- <input type="hidden" name="fromDataEditingPage" value="1">
- <input type="hidden" name="trait_type" value="ProbeSet">
- <input type="hidden" name="valsHidden" value="OFF">
- <input type="hidden" name="fullname" value="HC_M2_0606_P::1441186_at">
- <input type="hidden" name="RISet" value="BXD">
- #}
- {% for key in hddn %}
- <input type="hidden" name="{{ key }}" value="{{ hddn[key] }}">
- {% endfor %}
- <div>
- <div style="font-size:14px;">
- <strong style="font-size:16px;">Trait Data and Analysis&nbsp;</strong> for Record ID 1441186_at
- </div>
- </div>
-
- <p class="sectionheader" id="title1" style="border-radius: 5px;">&nbsp;&nbsp;Details and Links</p>
-
- <p id="sectionbody1"></p>
-
- <table class="collap" id="target1" style="margin-left:20px;" cellpadding="2" width="840" valign="top">
- <tr>
- <td class="fwb fs13" nowrap="on" valign="top" width="90">Gene Symbol:</td>
-
- <td valign="top" width="10"></td>
-
- <td valign="top" width="740"><span class="fs13 fsI">{{ this_trait.symbol }}</span></td>
- </tr>
-
- <tr>
- <td class="fwb fs13" nowrap="on" valign="top">Aliases:</td>
-
- <td valign="top" width="10"></td>
-
- <td valign="top"><span class="fs13 fsI">{{ this_trait.alias_fmt }}</span></td>
- </tr>
-
- <tr>
- <td class="fwb fs13" nowrap="on" valign="top">Description:</td>
-
- <td valign="top" width="10"></td>
-
- <td valign="top"><span class="fs13">{{ this_trait.description_fmt }}</span></td>
- </tr>
-
- <tr>
- <td class="fwb fs13" nowrap="on" valign="top">Location:</td>
-
- <td valign="top" width="10"></td>
-
- <td valign="top"><span class="fs13">{{ this_trait.location_fmt }}<br></span></td>
- </tr>
-
- <tr>
- <td class="fwb fs13" nowrap="on" valign="top">Target Score:</td>
-
- <td valign="top" width="10"></td>
-
- <td valign="top">
- <span class="fs13">
- <a href="/blatInfo.html" target="_blank" class="non_bold" title="Values higher than 2 for the specificity are good">
- BLAT specificity
- </a>: {{ "%.1f" % (this_trait.probe_set_specificity) }}&nbsp;&nbsp;&nbsp;
- Score: {{ "%i" % (this_trait.probe_set_blat_score) }}&nbsp;&nbsp;
- </span>
- </td>
- </tr>
-
- <tr>
- <td class="fwb fs13" nowrap="on" valign="top">Species and Group:</td>
-
- <td valign="top" width="10"></td>
-
- <td valign="top"><span class="fs13">{{ this_trait.species.capitalize() }}, {{fd.RISet}}</span></td>
- </tr>
-
- <tr>
- <td class="fs13 fwb" nowrap="on" valign="top">Database:</td>
-
- <td valign="top" width="10"></td>
-
- <td valign="top">
- <a href="{{ this_trait.database.url }}" target="_blank" class="fs13 fwn non_bold">{{ this_trait.database.name }}</a>
- </td>
- </tr>
-
- <tr>
- <td colspan="3" height="6"></td>
- </tr>
-
- <tr>
- <td class="fwb fs13" nowrap="on" valign="top">Resource Links:</td>
+ <td valign="top"><span class="fs13">{{ this_trait.description_fmt }}</span></td>
+ </tr>
- <td valign="top" width="10"></td>
+ <tr>
+ <td class="fwb fs13" nowrap="on" valign="top">Location:</td>
- <td valign="top">
- <span class="fs13">
- <span style="background:#dddddd;padding:2">
- <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&amp;cmd=Retrieve&amp;dopt=Graphics&amp;list_uids=20689" target="_blank" class=
- "fs14 fwn" title="Info from NCBI Entrez Gene">
- Gene
- </a>
+ <td valign="top" width="10"></td>
+
+ <td valign="top"><span class="fs13">{{ this_trait.location_fmt }}<br></span></td>
+ </tr>
+
+ <tr>
+ <td class="fwb fs13" nowrap="on" valign="top">Target Score:</td>
+
+ <td valign="top" width="10"></td>
+
+ <td valign="top">
+ <span class="fs13">
+ <a href="/blatInfo.html" target="_blank" class="non_bold" title="Values higher than 2 for the specificity are good">
+ BLAT specificity
+ </a>: {{ "%.1f" % (this_trait.probe_set_specificity) }}&nbsp;&nbsp;&nbsp;
+ Score: {{ "%i" % (this_trait.probe_set_blat_score) }}&nbsp;&nbsp;
</span>
- &nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
- "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&amp;CID=215917" target="_blank" class="fs14 fwn" title=
- "UniGene ID">UniGene</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
- "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&amp;cmd=search&amp;doptcmdl=DocSum&amp;term=BM119035" target="_blank" class=
- "fs14 fwn" title="Find the original GenBank sequence used to design the probes">GenBank</a></span>&nbsp;&nbsp;<span style=
- "background:#dddddd;padding:2"><a href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&amp;Cmd=DetailsSearch&amp;Term=18142"
- target="_blank" class="fs14 fwn" title="Find similar genes in other species">HomoloGene</a></span>&nbsp;&nbsp;</span></td>
- </tr>
-
- <tr>
- <td colspan="3" height="6"></td>
- </tr>
-
- <tr>
- <td></td>
-
- <td valign="top" width="10"></td>
-
- <td valign="top"><span style="font-family:verdana,serif;font-size:13px"><span style="background:#dddddd;padding:2"><a href=
- "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=mm9&amp;hgg_gene=NM_178280&amp;hgg_chrom=chr18&amp;hgg_start=81163112&amp;hgg_end=81183317"
- target="mainFrame" class="fs14 fwn" title="Info from UCSC Genome Browser">UCSC</a></span>&nbsp;&nbsp;<span style=
- "background:#dddddd;padding:2"><a href="http://biogps.gnf.org/?org=mouse#goto=genereport&amp;id=20689" target="mainFrame" class="fs14 fwn"
- title="Expression across many tissues and cell types">BioGPS</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
- "http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=Sall3" target="mainFrame" class="fs14 fwn" title=
- "Protein interactions: known and inferred">STRING</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
- "http://www.pantherdb.org/genes/gene.do?acc=20689" target="mainFrame" class="fs14 fwn" title=
- "Gene and protein data resources from Celera-ABI">PANTHER</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
- "http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=20689" target="mainFrame" class="fs14 fwn" title=
- "Meta-analysis of gene expression data">Gemma</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
- "http://lily.uthsc.edu:8080/20091027_GNInterfaces/20091027_redirectSynDB.jsp?query=Sall3" target="mainFrame" class="fs14 fwn" title=
- "Brain synapse database">SynDB</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
- "http://mouse.brain-map.org/brain/Sall3.html" target="mainFrame" class="fs14 fwn" title=
- "Allen Brain Atlas">ABA</a></span>&nbsp;&nbsp;</span></td>
- </tr>
- </table><br>
-
- <table class="collap" id="target1" cellpadding="2" width="620">
- <tr style="vertical-align:bottom;">
- <td align="center"><a href="#redirect" onclick=
- "addRmvSelection('BXD', document.getElementsByName('dataInput')[0], 'addToSelection');"><img src="/images/add_icon.jpg" alt=
- "Add To Collection" name="addselect" style="border:none;" title="Add To Collection"></a></td>
-
- <td align="center"><a href="#redirect" onclick=
- "openNewWin('/webqtl/main.py?cmd=sch&amp;gene=Sall3&amp;alias=1&amp;species=mouse')"><img src="/images/find_icon.jpg" alt=
- " Find similar expression data " name="addselect" style="border:none;" title=" Find similar expression data "></a></td>
-
- <td align="center"><a href="#redirect" onclick=
- "openNewWin('http://genome.ucsc.edu/cgi-bin/hgBlat?org=mouse&amp;db=mm9&amp;type=0&amp;sort=0&amp;output=0&amp;userSeq=%3E1441186_at%0AGAATTAGTTTTTTCAGTGCTGGGCAGGCCCTGTAAGTGCATGCCGGACAATGTTGCTTTACATCTGCCATGGAAGAGACTCTACAGCGTCCAAAGATGGCCACACCGGGTTTGCCTCACTGGGTGATCACAGTAGCGTTCAGGTCACTACAGCCAAGGGCTTCTCAGATCCATGTAGGAAAGAACAAGCGAGTGCTCACAGATACCACGCTCAGCAGACTTCATTAGCATTGTCTCACAGATAACAT%0A%3EProbe_522467%0AGAATTAGTTTTTTCAGTGCTGGGCA%0A%3EProbe_711755%0AGGCCCTGTAAGTGCATGCCGGACAA%0A%3EProbe_392797%0ATGTTGCTTTACATCTGCCATGGAAG%0A%3EProbe_246123%0AAGAGACTCTACAGCGTCCAAAGATG%0A%3EProbe_X80217%0AAAAGATGGCCACACCGGGTTTGCCT%0A%3EProbe_248315%0ACACTGGGTGATCACAGTAGCGTTCA%0A%3EProbe_349625%0AGTAGCGTTCAGGTCACTACAGCCAA%0A%3EProbe_288681%0AGGGCTTCTCAGATCCATGTAGGAAA%0A%3EProbe_801497%0AGAACAAGCGAGTGCTCACAGATACC%0A%3EProbe_139197%0AACAGATACCACGCTCAGCAGACTTC%0A%3EProbe_752Y13%0AATTAGCATTGTCTCACAGATAACAT%0A')">
- <img src="/images/verify_icon.jpg" alt=" Check probe locations at UCSC " name="addselect" style="border:none;" title=
- " Check probe locations at UCSC "></a></td>
-
- <td align="center"><a href="#redirect" onclick="openNewWin('/webqtl/main.py?FormID=geneWiki&amp;symbol=Sall3')"><img src=
- "/images/genewiki_icon.jpg" alt=" Write or review comments about this gene " name="addselect" style="border:none;" title=
- " Write or review comments about this gene "></a></td>
-
- <td align="center"><a href="#redirect" onclick=
- "openNewWin('/webqtl/main.py?FormID=SnpBrowserResultPage&amp;submitStatus=1&amp;diffAlleles=True&amp;customStrain=True&amp;geneName=Sall3')">
- <img src="/images/snp_icon.jpg" alt=" View SNPs and Indels " name="addselect" style="border:none;" title=" View SNPs and Indels "></a></td>
-
- <td align="center"><a href="#redirect" onclick=
- "openNewWin('http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=mouse&amp;db=mm9&amp;type=0&amp;sort=0&amp;output=0&amp;userSeq=%3E1441186_at%0AGAATTAGTTTTTTCAGTGCTGGGCAGGCCCTGTAAGTGCATGCCGGACAATGTTGCTTTACATCTGCCATGGAAGAGACTCTACAGCGTCCAAAGATGGCCACACCGGGTTTGCCTCACTGGGTGATCACAGTAGCGTTCAGGTCACTACAGCCAAGGGCTTCTCAGATCCATGTAGGAAAGAACAAGCGAGTGCTCACAGATACCACGCTCAGCAGACTTCATTAGCATTGTCTCACAGATAACAT%0A%3EProbe_522467%0AGAATTAGTTTTTTCAGTGCTGGGCA%0A%3EProbe_711755%0AGGCCCTGTAAGTGCATGCCGGACAA%0A%3EProbe_392797%0ATGTTGCTTTACATCTGCCATGGAAG%0A%3EProbe_246123%0AAGAGACTCTACAGCGTCCAAAGATG%0A%3EProbe_X80217%0AAAAGATGGCCACACCGGGTTTGCCT%0A%3EProbe_248315%0ACACTGGGTGATCACAGTAGCGTTCA%0A%3EProbe_349625%0AGTAGCGTTCAGGTCACTACAGCCAA%0A%3EProbe_288681%0AGGGCTTCTCAGATCCATGTAGGAAA%0A%3EProbe_801497%0AGAACAAGCGAGTGCTCACAGATACC%0A%3EProbe_139197%0AACAGATACCACGCTCAGCAGACTTC%0A%3EProbe_752Y13%0AATTAGCATTGTCTCACAGATAACAT%0A')">
- <img src="/images/rnaseq_icon.jpg" alt=" View probes, SNPs, and RNA-seq at UTHSC " name="addselect" style="border:none;" title=
- " View probes, SNPs, and RNA-seq at UTHSC "></a></td>
-
- <td align="center"><a href="#redirect" onclick=
- "openNewWin('/webqtl/main.py?FormID=showProbeInfo&amp;database=HC_M2_0606_P&amp;ProbeSetID=1441186_at&amp;CellID=&amp;RISet=BXD&amp;incparentsf1=ON')">
- <img src="/images/probe_icon.jpg" alt=" Check sequence of probes " name="addselect" style="border:none;" title=
- " Check sequence of probes "></a></td>
-
- <td align="center"></td>
- </tr>
-
- <tr style="vertical-align:bottom;">
- <td align="center">Add</td>
-
- <td align="center">Find</td>
-
- <td align="center">Verify</td>
-
- <td align="center">GeneWiki</td>
-
- <td align="center">SNPs</td>
-
- <td align="center">RNA-seq</td>
-
- <td align="center">Probes</td>
-
- <td align="center"></td>
- </tr>
- </table>
-
- <p class="sectionheader" id="title2" style="border-radius: 5px;">&nbsp;&nbsp;Basic Statistics</p>
-
-
- <p id="sectionbody2"></p>Include:
- <select name="corr_samples_group" size="1">
- {% for group, pretty_group in sample_group_types.items() %}
- <option value="{{ group }}">
- {{ pretty_group }}
- </option>
- {% endfor %}
- </select><br>
- <br>
- <input type="button" name="Default_Name" class="btn update" value=" Update Figures "><br>
- <br>
- <script language="Javascript" type="text/javascript">
-<!--
+ </td>
+ </tr>
- //$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});
+ <tr>
+ <td class="fwb fs13" nowrap="on" valign="top">Species and Group:</td>
- //-->
- </script>
+ <td valign="top" width="10"></td>
- <table cellpadding="0" cellspacing="0" border="0" class="display" id="stats_dyn"></table>
+ <td valign="top"><span class="fs13">{{ this_trait.species.capitalize() }}, {{fd.RISet}}</span></td>
+ </tr>
- <table class="target2" cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td>
- {% for sd in stats_data %}
- <div class="ui-tabs" id="{{ 'stats_tabs%i' % loop.index0 }}">
- <ul>
- <li><a href="#statstabs-1" class="stats_tab">Basic Table</a></li>
+ <tr>
+ <td class="fs13 fwb" nowrap="on" valign="top">Database:</td>
- <li><a href="#statstabs-5" class="stats_tab">Probability Plot</a></li>
+ <td valign="top" width="10"></td>
- <li><a href="#statstabs-3" class="stats_tab">Bar Graph (by name)</a></li>
+ <td valign="top">
+ <a href="{{ this_trait.database.url }}" target="_blank" class="fs13 fwn non_bold">{{ this_trait.database.name }}</a>
+ </td>
+ </tr>
- <li><a href="#statstabs-4" class="stats_tab">Bar Graph (by rank)</a></li>
+ <tr>
+ <td colspan="3" height="6"></td>
+ </tr>
- <li><a href="#statstabs-2" class="stats_tab">Box Plot</a></li>
- </ul>
+ <tr>
+ <td class="fwb fs13" nowrap="on" valign="top">Resource Links:</td>
- <div id="statstabs-1">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td>
- <table cellpadding="20" cellspacing="0">
- <tr>
- <td class="fs14 fwb ffl b1 cw cbrb" align="left" width="180">Statistic</td>
+ <td valign="top" width="10"></td>
- <td class="fs14 fwb ffl b1 cw cbrb" align="right" width="60">Value</td>
- </tr>
+ <td valign="top">
+ <span class="fs13">
+ <span style="background:#dddddd;padding:2">
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&amp;cmd=Retrieve&amp;dopt=Graphics&amp;list_uids=20689" target="_blank" class=
+ "fs14 fwn" title="Info from NCBI Entrez Gene">
+ Gene
+ </a>
+ </span>
+ &nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
+ "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&amp;CID=215917" target="_blank" class="fs14 fwn" title=
+ "UniGene ID">UniGene</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
+ "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&amp;cmd=search&amp;doptcmdl=DocSum&amp;term=BM119035" target="_blank" class=
+ "fs14 fwn" title="Find the original GenBank sequence used to design the probes">GenBank</a></span>&nbsp;&nbsp;<span style=
+ "background:#dddddd;padding:2"><a href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&amp;Cmd=DetailsSearch&amp;Term=18142"
+ target="_blank" class="fs14 fwn" title="Find similar genes in other species">HomoloGene</a></span>&nbsp;&nbsp;</span></td>
+ </tr>
+
+ <tr>
+ <td colspan="3" height="6"></td>
+ </tr>
+
+ <tr>
+ <td></td>
+
+ <td valign="top" width="10"></td>
+
+ <td valign="top"><span style="font-family:verdana,serif;font-size:13px"><span style="background:#dddddd;padding:2"><a href=
+ "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=mm9&amp;hgg_gene=NM_178280&amp;hgg_chrom=chr18&amp;hgg_start=81163112&amp;hgg_end=81183317"
+ target="mainFrame" class="fs14 fwn" title="Info from UCSC Genome Browser">UCSC</a></span>&nbsp;&nbsp;<span style=
+ "background:#dddddd;padding:2"><a href="http://biogps.gnf.org/?org=mouse#goto=genereport&amp;id=20689" target="mainFrame" class="fs14 fwn"
+ title="Expression across many tissues and cell types">BioGPS</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
+ "http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=Sall3" target="mainFrame" class="fs14 fwn" title=
+ "Protein interactions: known and inferred">STRING</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
+ "http://www.pantherdb.org/genes/gene.do?acc=20689" target="mainFrame" class="fs14 fwn" title=
+ "Gene and protein data resources from Celera-ABI">PANTHER</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
+ "http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=20689" target="mainFrame" class="fs14 fwn" title=
+ "Meta-analysis of gene expression data">Gemma</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
+ "http://lily.uthsc.edu:8080/20091027_GNInterfaces/20091027_redirectSynDB.jsp?query=Sall3" target="mainFrame" class="fs14 fwn" title=
+ "Brain synapse database">SynDB</a></span>&nbsp;&nbsp;<span style="background:#dddddd;padding:2"><a href=
+ "http://mouse.brain-map.org/brain/Sall3.html" target="mainFrame" class="fs14 fwn" title=
+ "Allen Brain Atlas">ABA</a></span>&nbsp;&nbsp;</span></td>
+ </tr>
+ </table><br>
+
+ <table class="collap" id="target1" cellpadding="2" width="620">
+ <tr style="vertical-align:bottom;">
+ <td align="center"><a href="#redirect" onclick=
+ "addRmvSelection('BXD', document.getElementsByName('dataInput')[0], 'addToSelection');"><img src="/images/add_icon.jpg" alt=
+ "Add To Collection" name="addselect" style="border:none;" title="Add To Collection"></a></td>
+
+ <td align="center"><a href="#redirect" onclick=
+ "openNewWin('/webqtl/main.py?cmd=sch&amp;gene=Sall3&amp;alias=1&amp;species=mouse')"><img src="/images/find_icon.jpg" alt=
+ " Find similar expression data " name="addselect" style="border:none;" title=" Find similar expression data "></a></td>
+
+ <td align="center"><a href="#redirect" onclick=
+ "openNewWin('http://genome.ucsc.edu/cgi-bin/hgBlat?org=mouse&amp;db=mm9&amp;type=0&amp;sort=0&amp;output=0&amp;userSeq=%3E1441186_at%0AGAATTAGTTTTTTCAGTGCTGGGCAGGCCCTGTAAGTGCATGCCGGACAATGTTGCTTTACATCTGCCATGGAAGAGACTCTACAGCGTCCAAAGATGGCCACACCGGGTTTGCCTCACTGGGTGATCACAGTAGCGTTCAGGTCACTACAGCCAAGGGCTTCTCAGATCCATGTAGGAAAGAACAAGCGAGTGCTCACAGATACCACGCTCAGCAGACTTCATTAGCATTGTCTCACAGATAACAT%0A%3EProbe_522467%0AGAATTAGTTTTTTCAGTGCTGGGCA%0A%3EProbe_711755%0AGGCCCTGTAAGTGCATGCCGGACAA%0A%3EProbe_392797%0ATGTTGCTTTACATCTGCCATGGAAG%0A%3EProbe_246123%0AAGAGACTCTACAGCGTCCAAAGATG%0A%3EProbe_X80217%0AAAAGATGGCCACACCGGGTTTGCCT%0A%3EProbe_248315%0ACACTGGGTGATCACAGTAGCGTTCA%0A%3EProbe_349625%0AGTAGCGTTCAGGTCACTACAGCCAA%0A%3EProbe_288681%0AGGGCTTCTCAGATCCATGTAGGAAA%0A%3EProbe_801497%0AGAACAAGCGAGTGCTCACAGATACC%0A%3EProbe_139197%0AACAGATACCACGCTCAGCAGACTTC%0A%3EProbe_752Y13%0AATTAGCATTGTCTCACAGATAACAT%0A')">
+ <img src="/images/verify_icon.jpg" alt=" Check probe locations at UCSC " name="addselect" style="border:none;" title=
+ " Check probe locations at UCSC "></a></td>
+
+ <td align="center"><a href="#redirect" onclick="openNewWin('/webqtl/main.py?FormID=geneWiki&amp;symbol=Sall3')"><img src=
+ "/images/genewiki_icon.jpg" alt=" Write or review comments about this gene " name="addselect" style="border:none;" title=
+ " Write or review comments about this gene "></a></td>
+
+ <td align="center"><a href="#redirect" onclick=
+ "openNewWin('/webqtl/main.py?FormID=SnpBrowserResultPage&amp;submitStatus=1&amp;diffAlleles=True&amp;customStrain=True&amp;geneName=Sall3')">
+ <img src="/images/snp_icon.jpg" alt=" View SNPs and Indels " name="addselect" style="border:none;" title=" View SNPs and Indels "></a></td>
- <tr align="right">
- <td class="fs13 b1 cbw c222" align="left">N of Samples</td>
+ <td align="center"><a href="#redirect" onclick=
+ "openNewWin('http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=mouse&amp;db=mm9&amp;type=0&amp;sort=0&amp;output=0&amp;userSeq=%3E1441186_at%0AGAATTAGTTTTTTCAGTGCTGGGCAGGCCCTGTAAGTGCATGCCGGACAATGTTGCTTTACATCTGCCATGGAAGAGACTCTACAGCGTCCAAAGATGGCCACACCGGGTTTGCCTCACTGGGTGATCACAGTAGCGTTCAGGTCACTACAGCCAAGGGCTTCTCAGATCCATGTAGGAAAGAACAAGCGAGTGCTCACAGATACCACGCTCAGCAGACTTCATTAGCATTGTCTCACAGATAACAT%0A%3EProbe_522467%0AGAATTAGTTTTTTCAGTGCTGGGCA%0A%3EProbe_711755%0AGGCCCTGTAAGTGCATGCCGGACAA%0A%3EProbe_392797%0ATGTTGCTTTACATCTGCCATGGAAG%0A%3EProbe_246123%0AAGAGACTCTACAGCGTCCAAAGATG%0A%3EProbe_X80217%0AAAAGATGGCCACACCGGGTTTGCCT%0A%3EProbe_248315%0ACACTGGGTGATCACAGTAGCGTTCA%0A%3EProbe_349625%0AGTAGCGTTCAGGTCACTACAGCCAA%0A%3EProbe_288681%0AGGGCTTCTCAGATCCATGTAGGAAA%0A%3EProbe_801497%0AGAACAAGCGAGTGCTCACAGATACC%0A%3EProbe_139197%0AACAGATACCACGCTCAGCAGACTTC%0A%3EProbe_752Y13%0AATTAGCATTGTCTCACAGATAACAT%0A')">
+ <img src="/images/rnaseq_icon.jpg" alt=" View probes, SNPs, and RNA-seq at UTHSC " name="addselect" style="border:none;" title=
+ " View probes, SNPs, and RNA-seq at UTHSC "></a></td>
+
+ <td align="center"><a href="#redirect" onclick=
+ "openNewWin('/webqtl/main.py?FormID=showProbeInfo&amp;database=HC_M2_0606_P&amp;ProbeSetID=1441186_at&amp;CellID=&amp;RISet=BXD&amp;incparentsf1=ON')">
+ <img src="/images/probe_icon.jpg" alt=" Check sequence of probes " name="addselect" style="border:none;" title=
+ " Check sequence of probes "></a></td>
- <td class="fs13 b1 cbw c222" nowrap="yes" id="n_of_samples_value">{{ sd.N }}</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Mean</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes" id="mean_value">{{ "%2.3f" % sd.traitmean }}</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Median</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes" id="median_value">{{ "%2.3f" % sd.traitmedian }}</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Error (SE)</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.traitsem }}</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Deviation (SD)</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.traitstdev }}</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Minimum</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.min }}</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Maximum</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.max }}</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Range (log2)</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.range_log2 }}</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span>Range (fold)</span></td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.range_fold }}</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span><a href="/glossary.html#Interquartile" target="_blank" class=
- "non_bold">Interquartile Range</a></span></td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.interquartile }} </td>
- </tr>
- </table>
- </td>
- </tr>
- </table>
- </div>
-
- <div id="statstabs-5">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td><img src="/image/nP_OE9u7BSx.gif" alt="nP_OE9u7BSx.gif" border="0"></td>
- </tr>
-
- <tr>
- <td><br>
- <br>
- This plot evaluates whether data are normally distributed. Different symbols represent different groups.<br>
- <br>
- More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot" target="_blank">Normal Probability Plots</a> and more
- about interpreting these plots from the <a href="/glossary.html#normal_probability" target="_blank">glossary</a></td>
- </tr>
- </table>
- </div>
-
- <div id="statstabs-2">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td align="left">
- <img src="/image/Box_gUFtEOVI.gif" alt="Box_gUFtEOVI.gif" border="0">
-
- <p><span>More about <a href="http://davidmlane.com/hyperstat/A37797.html" target="_blank" class="fs13">Box Plots</a></span></p>
- </td>
- </tr>
- </table>
- </div>
-
- <div id="statstabs-3">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td><img src="/image/Bar_y7L2rYlL.gif" alt="Bar_y7L2rYlL.gif" border="0"></td>
- </tr>
- </table>
- </div>
-
- <div id="statstabs-4">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td><img src="/image/Bar_1Z4GjYFq.gif" alt="Bar_1Z4GjYFq.gif" border="0"></td>
- </tr>
- </table>
- </div>
- </div>
- {% endfor %}
- {# Not used now - Todo: Delete after we're sure this is right.
- <div class="ui-tabs" id="stats_tabs1">
- <ul>
- <li><a href="#statstabs-1" class="stats_tab">Basic Table</a></li>
+ <td align="center"></td>
+ </tr>
- <li><a href="#statstabs-5" class="stats_tab">Probability Plot</a></li>
+ <tr style="vertical-align:bottom;">
+ <td align="center">Add</td>
- <li><a href="#statstabs-3" class="stats_tab">Bar Graph (by name)</a></li>
+ <td align="center">Find</td>
- <li><a href="#statstabs-4" class="stats_tab">Bar Graph (by rank)</a></li>
+ <td align="center">Verify</td>
- <li><a href="#statstabs-2" class="stats_tab">Box Plot</a></li>
- </ul>
+ <td align="center">GeneWiki</td>
- <div id="statstabs-1">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td>
- <table cellpadding="20" cellspacing="0">
- <tr>
- <td class="fs14 fwb ffl b1 cw cbrb" align="left" width="180">Statistic</td>
+ <td align="center">SNPs</td>
- <td class="fs14 fwb ffl b1 cw cbrb" align="right" width="60">Value</td>
- </tr>
+ <td align="center">RNA-seq</td>
- <tr align="right">
- <td class="fs13 b1 cbw c222" align="left">N of Samples</td>
+ <td align="center">Probes</td>
- <td class="fs13 b1 cbw c222" nowrap="yes">71</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Mean</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">6.109</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Median</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">6.084</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Error (SE)</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">0.022</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Deviation (SD)</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">0.187</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Minimum</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">5.782</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Maximum</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">6.579</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Range (log2)</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">0.797</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span>Range (fold)</span></td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">1.74</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span><a href="/glossary.html#Interquartile" target="_blank" class=
- "non_bold">Interquartile Range</a></span></td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">1.13</td>
- </tr>
- </table>
- </td>
- </tr>
- </table>
- </div>
-
- <div id="statstabs-5">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td><img src="/image/nP_eSYO7ZQg.gif" alt="nP_eSYO7ZQg.gif" border="0"></td>
- </tr>
-
- <tr>
- <td><br>
- <br>
- This plot evaluates whether data are normally distributed. Different symbols represent different groups.<br>
- <br>
- More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot" target="_blank">Normal Probability Plots</a> and more
- about interpreting these plots from the <a href="/glossary.html#normal_probability" target="_blank">glossary</a></td>
- </tr>
- </table>
- </div>
-
- <div id="statstabs-2">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td align="left">
- <img src="/image/Box_PWNWQMfj.gif" alt="Box_PWNWQMfj.gif" border="0">
-
- <p><span>More about <a href="http://davidmlane.com/hyperstat/A37797.html" target="_blank" class="fs13">Box Plots</a></span></p>
- </td>
- </tr>
- </table>
- </div>
-
- <div id="statstabs-3">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td><img src="/image/Bar_VuPqYbR6.gif" alt="Bar_VuPqYbR6.gif" border="0"></td>
- </tr>
- </table>
- </div>
-
- <div id="statstabs-4">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td><img src="/image/Bar_9PbdvXZ9.gif" alt="Bar_9PbdvXZ9.gif" border="0"></td>
- </tr>
- </table>
- </div>
- </div>
+ <td align="center"></td>
+ </tr>
+ </table>
- <div class="ui-tabs" id="stats_tabs2">
+ <p class="sectionheader" id="title2" style="border-radius: 5px;">&nbsp;&nbsp;Basic Statistics</p>
- <ul>
- <li><a href="#statstabs-1" class="stats_tab">Basic Table</a></li>
+ <p id="sectionbody2"></p>Include:
+ <select name="corr_samples_group" size="1">
+ {% for group, pretty_group in sample_group_types.items() %}
+ <option value="{{ group }}">
+ {{ pretty_group }}
+ </option>
+ {% endfor %}
+ </select><br>
+ <br>
+ <input type="button" name="Default_Name" class="btn update" value=" Update Figures "><br>
+ <br>
+ <script language="Javascript" type="text/javascript">
+ <!--
- <li><a href="#statstabs-5" class="stats_tab">Probability Plot</a></li>
+ //$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});
- <li><a href="#statstabs-3" class="stats_tab">Bar Graph (by name)</a></li>
+ //
+ -->
+ </script>
- <li><a href="#statstabs-4" class="stats_tab">Bar Graph (by rank)</a></li>
+ <table cellpadding="0" cellspacing="0" border="0" class="display" id="stats_dyn"></table>
- <li><a href="#statstabs-2" class="stats_tab">Box Plot</a></li>
- </ul>
+ <table class="target2" cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td>
+ {% for sd in stats_data %}
+ <div class="ui-tabs" id="{{ 'stats_tabs%i' % loop.index0 }}">
+ <ul>
+ <li><a href="#statstabs-1" class="stats_tab">Basic Table</a></li>
- <div id="statstabs-1">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td>
- <table cellpadding="20" cellspacing="0">
- <tr>
- <td class="fs14 fwb ffl b1 cw cbrb" align="left" width="180">Statistic</td>
+ <li><a href="#statstabs-5" class="stats_tab">Probability Plot</a></li>
- <td class="fs14 fwb ffl b1 cw cbrb" align="right" width="60">Value</td>
- </tr>
+ <li><a href="#statstabs-3" class="stats_tab">Bar Graph (by name)</a></li>
- <tr align="right">
- <td class="fs13 b1 cbw c222" align="left">N of Samples</td>
+ <li><a href="#statstabs-4" class="stats_tab">Bar Graph (by rank)</a></li>
- <td class="fs13 b1 cbw c222" nowrap="yes">32</td>
- </tr>
+ <li><a href="#statstabs-2" class="stats_tab">Box Plot</a></li>
+ </ul>
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Mean</td>
+ <div id="statstabs-1">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td>
+ <table cellpadding="20" cellspacing="0">
+ <tr>
+ <td class="fs14 fwb ffl b1 cw cbrb" align="left" width="180">Statistic</td>
- <td class="fs13 b1 cbw c222" nowrap="yes">6.176</td>
- </tr>
+ <td class="fs14 fwb ffl b1 cw cbrb" align="right" width="60">Value</td>
+ </tr>
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Median</td>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" align="left">N of Samples</td>
- <td class="fs13 b1 cbw c222" nowrap="yes">6.170</td>
- </tr>
+ <td class="fs13 b1 cbw c222" nowrap="yes" id="n_of_samples_value">{{ sd.N }}</td>
+ </tr>
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Error (SE)</td>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Mean</td>
- <td class="fs13 b1 cbw c222" nowrap="yes">0.027</td>
- </tr>
+ <td class="fs13 b1 cbw c222" nowrap="yes" id="mean_value">{{ "%2.3f" % sd.traitmean }}</td>
+ </tr>
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Deviation (SD)</td>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Median</td>
- <td class="fs13 b1 cbw c222" nowrap="yes">0.150</td>
- </tr>
+ <td class="fs13 b1 cbw c222" nowrap="yes" id="median_value">{{ "%2.3f" % sd.traitmedian }}</td>
+ </tr>
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Minimum</td>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Error (SE)</td>
- <td class="fs13 b1 cbw c222" nowrap="yes">5.906</td>
- </tr>
+ <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.traitsem }}</td>
+ </tr>
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Maximum</td>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Deviation (SD)</td>
- <td class="fs13 b1 cbw c222" nowrap="yes">6.485</td>
- </tr>
+ <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.traitstdev }}</td>
+ </tr>
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Range (log2)</td>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Minimum</td>
- <td class="fs13 b1 cbw c222" nowrap="yes">0.579</td>
- </tr>
+ <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.min }}</td>
+ </tr>
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span>Range (fold)</span></td>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Maximum</td>
- <td class="fs13 b1 cbw c222" nowrap="yes">1.49</td>
- </tr>
+ <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.max }}</td>
+ </tr>
- <tr align="right">
- <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span><a href="/glossary.html#Interquartile" target="_blank" class=
- "non_bold">Interquartile Range</a></span></td>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Range (log2)</td>
- <td class="fs13 b1 cbw c222" nowrap="yes">1.15</td>
- </tr>
- </table>
- </td>
- </tr>
- </table>
- </div>
+ <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.range_log2 }}</td>
+ </tr>
- <div id="statstabs-5">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td><img src="/image/nP_swDAFlJy.gif" alt="nP_swDAFlJy.gif" border="0"></td>
- </tr>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span>Range (fold)</span></td>
- <tr>
- <td><br>
- <br>
- This plot evaluates whether data are normally distributed. Different symbols represent different groups.<br>
- <br>
- More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot" target="_blank">Normal Probability Plots</a> and more
- about interpreting these plots from the <a href="/glossary.html#normal_probability" target="_blank">glossary</a></td>
- </tr>
- </table>
- </div>
-
- <div id="statstabs-2">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td align="left">
- <img src="/image/Box_6sQJ8xhK.gif" alt="Box_6sQJ8xhK.gif" border="0">
-
- <p><span>More about <a href="http://davidmlane.com/hyperstat/A37797.html" target="_blank" class="fs13">Box Plots</a></span></p>
- </td>
- </tr>
- </table>
- </div>
-
- <div id="statstabs-3">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td><img src="/image/Bar_QMWE2VEp.gif" alt="Bar_QMWE2VEp.gif" border="0"></td>
- </tr>
- </table>
- </div>
-
- <div id="statstabs-4">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td><img src="/image/Bar_X07QmgsX.gif" alt="Bar_X07QmgsX.gif" border="0"></td>
- </tr>
- </table>
- </div>
- </div>
- </td>
- </tr>
- </table>
- #}
+ <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.range_fold }}</td>
+ </tr>
- <p class="sectionheader" id="title3" style="border-radius: 5px;">&nbsp;&nbsp;Calculate Correlations</p>
-
- <p id="sectionbody3"></p>
-
- <table class="target4" cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td>
- <div class="ui-tabs" id="corr_tabs">
- <div id="corrtabs-1">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td>
- <input type="hidden" name="orderBy" value="2">
-
- <table cellpadding="2" cellspacing="0" width="619px">
- <tr>
- <td><span class="ff1 fwb fs12">Method:</span></td>
- <td colspan="3">
- <select name="corr_method" size="1">
- <option value="sample">Sample r</option>
- <option value="lit">Literature r</option>
- <option value="tissue">Tissue r</option>
- </select>
- </td>
- </tr>
- <tr>
- <td><span class="ffl fwb fs12">Database:</span></td>
- <td colspan="3">
- <select name="corr_dataset" size="1">
- {% for tissue in corr_tools.dataset_menu %}
- {% if tissue.tissue %}
- <optgroup label="{{ tissue.tissue }} ------">
- {% endif %}
- {% for dataset in tissue.datasets %}
- <option value="{{ dataset[1] }}"
- {% if corr_tools.dataset_menu_selected == dataset[1] %}
- selected
- {% endif %}>
- {{ dataset[0] }}
- </option>
- {% endfor %}
- {% if tissue.tissue %}
- </optgroup>
- {% endif %}
- {% endfor %}
- </select>
- </td>
- </tr>
-
-
- <tr>
- <td><span class="ffl fwb fs12">Return:</span></td>
-
- <td><select name="corr_return_results" size="1">
- {% for return_result in corr_tools.return_results_menu %}
- <option value="{{ return_result }}"
- {% if corr_tools.return_results_menu_selected == return_result %}
- selected
- {% endif %}>
- Top {{ return_result }}
- </option>
- {% endfor %}
- </select></td>
- </tr>
-
-
- <tr class="mdp1">
- <td><span class="ffl fwb fs12">Samples:</span></td>
- <td>
- <select name="corr_samples_group" size="1">
- {% for group, pretty_group in sample_group_types.items() %}
- <option value="{{ group }}">
- {{ pretty_group }}
- </option>
- {% endfor %}
- </select>
- </td>
- </tr>
-
- </table>
- <br>
- <div id="corr_sample_method_options">
- Pearson <input type="radio" name="corr_sample_method" value="pearson" checked>
- &nbsp;&nbsp;&nbsp;
- Spearman Rank <input type="radio" name="corr_sample_method" value="spearman">
- </div>
- <br>
-
- <input type="submit" name="corr_compute" id="corr_compute" class="btn" value="Compute"><br><br>
-
- <span id="sample_r_desc" class="correlation_desc fs12">
- The <a href="/correlationAnnotation.html#sample_r" target="_blank">Sample Correlation</a>
- is computed
- between trait data and any<br>
- other traits in the sample database selected above. Use
- <a href="/glossary.html#Correlations" target="_blank">Spearman
- Rank</a><br>
- when the sample size is small (&lt;20) or when there are influential outliers.
- </span>
- <SPAN id="lit_r_desc" style="display: none;" class="correlation_desc fs12">
- The <A HREF="/correlationAnnotation.html" TARGET="_blank">Literature Correlation</A>
- (Lit r) between
- this gene and all other genes is computed<BR>
- using the <A HREF="https://grits.eecs.utk.edu/sgo/sgo.html" TARGET="_blank">
- Semantic Gene Organizer</A>
- and human, rat, and mouse data from PubMed. <BR>
- Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<BR><BR>
- <A HREF="/glossary.html#Literature" TARGET="_blank">More on using Lit r</A>
- </SPAN>
- <SPAN id="tissue_r_desc" style="display: none;" class="correlation_desc fs12">
- The <A HREF="/webqtl/main.py?FormID=tissueCorrelation" TARGET="_blank">Tissue Correlation</A>
- (Tissue r)
- estimates the similarity of expression of two genes<BR>
- or transcripts across different cells, tissues, or organs
- (<A HREF="/correlationAnnotation.html#tissue_r" TARGET="_blank">glossary</A>).
- Tissue correlations<BR>
- are generated by analyzing expression in multiple samples usually taken from single cases.<BR>
- <STRONG>Pearson</STRONG> and <STRONG>Spearman Rank</STRONG> correlations have been
- computed for all pairs of genes<BR> using data from mouse samples.<BR>
- </SPAN>
-
- <br>
- </td>
- </tr>
- </table>
- </div>
- </div>
- </td>
- </tr>
- </table>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span><a href="/glossary.html#Interquartile" target="_blank" class=
+ "non_bold">Interquartile Range</a></span></td>
- <p class="sectionheader" id="title4" style="border-radius: 5px;">&nbsp;&nbsp;Mapping Tools</p>
+ <td class="fs13 b1 cbw c222" nowrap="yes">{{ "%2.3f" % sd.interquartile }} </td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
+ </div>
- <p id="sectionbody4"></p><script language="Javascript" type="text/javascript">
-<!--
+ <div id="statstabs-5">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td><img src="/image/nP_OE9u7BSx.gif" alt="nP_OE9u7BSx.gif" border="0"></td>
+ </tr>
+
+ <tr>
+ <td><br>
+ <br>
+ This plot evaluates whether data are normally distributed. Different symbols represent different groups.<br>
+ <br>
+ More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot" target="_blank">Normal Probability Plots</a> and more
+ about interpreting these plots from the <a href="/glossary.html#normal_probability" target="_blank">glossary</a></td>
+ </tr>
+ </table>
+ </div>
- //$(function() { $("#mapping_tabs").tabs(); });
+ <div id="statstabs-2">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td align="left">
+ <img src="/image/Box_gUFtEOVI.gif" alt="Box_gUFtEOVI.gif" border="0">
- //-->
- </script>
+ <p><span>More about <a href="http://davidmlane.com/hyperstat/A37797.html" target="_blank" class="fs13">Box Plots</a></span></p>
+ </td>
+ </tr>
+ </table>
+ </div>
- <table class="target2" cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td>
- <div class="ui-tabs" id="mapping_tabs">
- <ul>
- <li><a href="#mappingtabs-1">Interval</a></li>
+ <div id="statstabs-3">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td><img src="/image/Bar_y7L2rYlL.gif" alt="Bar_y7L2rYlL.gif" border="0"></td>
+ </tr>
+ </table>
+ </div>
- <li><a href="#mappingtabs-2">Marker Regression</a></li>
+ <div id="statstabs-4">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td><img src="/image/Bar_1Z4GjYFq.gif" alt="Bar_1Z4GjYFq.gif" border="0"></td>
+ </tr>
+ </table>
+ </div>
+ </div>
+ {% endfor %}
+ {# Not used now - Todo: Delete after we're sure this is right.
+ <div class="ui-tabs" id="stats_tabs1">
+ <ul>
+ <li><a href="#statstabs-1" class="stats_tab">Basic Table</a></li>
- <li><a href="#mappingtabs-3">Composite</a></li>
+ <li><a href="#statstabs-5" class="stats_tab">Probability Plot</a></li>
- <li><a href="#mappingtabs-4">Pair-Scan</a></li>
- </ul>
+ <li><a href="#statstabs-3" class="stats_tab">Bar Graph (by name)</a></li>
- <div id="mappingtabs-1">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td class="fs12 fwn" nowrap="on" valign="top">
- <table cellpadding="2" cellspacing="0" width="263px">
- <tr>
- <td><span class="ffl fwb fs12">Chromosome:</span></td>
+ <li><a href="#statstabs-4" class="stats_tab">Bar Graph (by rank)</a></li>
- <td colspan="3"><select name="chromosomes1" size="1">
- <option value="-1">
- All
- </option>
+ <li><a href="#statstabs-2" class="stats_tab">Box Plot</a></li>
+ </ul>
- <option value="0">
- 1
- </option>
+ <div id="statstabs-1">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td>
+ <table cellpadding="20" cellspacing="0">
+ <tr>
+ <td class="fs14 fwb ffl b1 cw cbrb" align="left" width="180">Statistic</td>
- <option value="1">
- 2
- </option>
+ <td class="fs14 fwb ffl b1 cw cbrb" align="right" width="60">Value</td>
+ </tr>
- <option value="2">
- 3
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" align="left">N of Samples</td>
- <option value="3">
- 4
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">71</td>
+ </tr>
- <option value="4">
- 5
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Mean</td>
- <option value="5">
- 6
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">6.109</td>
+ </tr>
- <option value="6">
- 7
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Median</td>
- <option value="7">
- 8
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">6.084</td>
+ </tr>
- <option value="8">
- 9
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Error (SE)</td>
- <option value="9">
- 10
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">0.022</td>
+ </tr>
- <option value="10">
- 11
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Deviation (SD)</td>
- <option value="11">
- 12
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">0.187</td>
+ </tr>
- <option value="12">
- 13
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Minimum</td>
- <option value="13">
- 14
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">5.782</td>
+ </tr>
- <option value="14">
- 15
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Maximum</td>
- <option value="15">
- 16
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">6.579</td>
+ </tr>
- <option value="16">
- 17
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Range (log2)</td>
- <option value="17">
- 18
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">0.797</td>
+ </tr>
- <option value="18">
- 19
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span>Range (fold)</span></td>
- <option value="19">
- X
- </option>
- </select></td>
- </tr>
+ <td class="fs13 b1 cbw c222" nowrap="yes">1.74</td>
+ </tr>
- <tr>
- <td><span class="ffl fwb fs12">Mapping Scale:</span></td>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span><a href="/glossary.html#Interquartile" target="_blank" class=
+ "non_bold">Interquartile Range</a></span></td>
- <td><select name="scale1" size="1" onchange=
- "checkUncheck(window.document.dataInput.scale1.value, window.document.dataInput.permCheck1, window.document.dataInput.bootCheck1)">
- <option value="physic">
- Megabase
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">1.13</td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
+ </div>
- <option value="morgan">
- Centimorgan
- </option>
- </select></td>
- </tr>
- </table><br>
- <input type="checkbox" name="permCheck1" class="checkbox" checked>Permutation Test (n=2000)<br>
- <input type="checkbox" name="bootCheck1" class="checkbox">Bootstrap Test (n=2000)<br>
- <input type="checkbox" name="parentsf14regression1" class="checkbox">Use Parents<br>
- <input type="checkbox" name="applyVarianceSE1" class="checkbox">Use Weighted<br>
- <br>
- <input type="button" name="interval" class="btn" value=" Compute "><br>
- <br>
- </td>
- </tr>
-
- <tr>
- <td valign="top"><span class="fs12"><a href="/glossary.html#intmap" target="_blank">Interval Mapping</a> computes linkage maps
- for the entire genome or single<br>
- chromosomes. The <a href="/glossary.html#permutation" target="_blank">Permutation Test</a> estimates suggestive and
- significant<br>
- linkage scores. The <a href="/glossary.html#bootstrap" target="_blank">Bootstrap Test</a> estimates the precision of the QTL
- location.</span><br></td>
- </tr>
- </table>
- </div>
-
- <div id="mappingtabs-2">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td class="fs12 fwn" nowrap="on" valign="top">
- <table cellpadding="2" cellspacing="0" width="263px">
- <tr>
- <td><span class="ffl fwb fs12"><strong>Display LRS greater than:</strong></span></td>
-
- <td><input type="text" name="suggestive" size="5" maxlength="8"></td>
- </tr>
-
- <tr>
- <td><input type="checkbox" name="displayAllLRS" class="checkbox"> <span class="ffl fs12">Display all LRS</span></td>
- </tr>
-
- <tr>
- <td><input type="checkbox" name="parentsf14regression2" class="checkbox"> <span class="ffl fs12">Use Parents</span></td>
- </tr>
-
- <tr>
- <td><input type="checkbox" name="applyVarianceSE2" class="checkbox"> <span class="ffl fs12">Use Weighted</span></td>
- </tr>
- </table><br>
- <input type="button" name="marker" class="btn" value=" Compute "><br>
- <br>
- </td>
- </tr>
-
- <tr>
- <td valign="top"><span class="fs12"><a href="/glossary.html#" target="_blank">Marker regression</a> computes and displays LRS
- values for individual markers.<br>
- This function also lists additive effects (phenotype units per allele) and<br>
- dominance deviations for some datasets.<br></span><br></td>
- </tr>
- </table>
- </div>
-
- <div id="mappingtabs-3">
- <table cellpadding="3" cellspacing="0" width="100%">
- <tr>
- <td class="fs12 fwn" nowrap="on" valign="top">
- <table cellpadding="2" cellspacing="0" width="325px">
- <tr>
- <td><span class="ffl fwb fs12">Chromosome:</span></td>
-
- <td colspan="3"><select name="chromosomes2" size="1">
- <option value="-1">
- All
- </option>
+ <div id="statstabs-5">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td><img src="/image/nP_eSYO7ZQg.gif" alt="nP_eSYO7ZQg.gif" border="0"></td>
+ </tr>
+
+ <tr>
+ <td><br>
+ <br>
+ This plot evaluates whether data are normally distributed. Different symbols represent different groups.<br>
+ <br>
+ More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot" target="_blank">Normal Probability Plots</a> and more
+ about interpreting these plots from the <a href="/glossary.html#normal_probability" target="_blank">glossary</a></td>
+ </tr>
+ </table>
+ </div>
- <option value="0">
- 1
- </option>
+ <div id="statstabs-2">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td align="left">
+ <img src="/image/Box_PWNWQMfj.gif" alt="Box_PWNWQMfj.gif" border="0">
- <option value="1">
- 2
- </option>
+ <p><span>More about <a href="http://davidmlane.com/hyperstat/A37797.html" target="_blank" class="fs13">Box Plots</a></span></p>
+ </td>
+ </tr>
+ </table>
+ </div>
- <option value="2">
- 3
- </option>
+ <div id="statstabs-3">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td><img src="/image/Bar_VuPqYbR6.gif" alt="Bar_VuPqYbR6.gif" border="0"></td>
+ </tr>
+ </table>
+ </div>
- <option value="3">
- 4
- </option>
+ <div id="statstabs-4">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td><img src="/image/Bar_9PbdvXZ9.gif" alt="Bar_9PbdvXZ9.gif" border="0"></td>
+ </tr>
+ </table>
+ </div>
+ </div>
- <option value="4">
- 5
- </option>
+ <div class="ui-tabs" id="stats_tabs2">
- <option value="5">
- 6
- </option>
- <option value="6">
- 7
- </option>
+ <ul>
+ <li><a href="#statstabs-1" class="stats_tab">Basic Table</a></li>
- <option value="7">
- 8
- </option>
+ <li><a href="#statstabs-5" class="stats_tab">Probability Plot</a></li>
- <option value="8">
- 9
- </option>
+ <li><a href="#statstabs-3" class="stats_tab">Bar Graph (by name)</a></li>
- <option value="9">
- 10
- </option>
+ <li><a href="#statstabs-4" class="stats_tab">Bar Graph (by rank)</a></li>
- <option value="10">
- 11
- </option>
+ <li><a href="#statstabs-2" class="stats_tab">Box Plot</a></li>
+ </ul>
- <option value="11">
- 12
- </option>
+ <div id="statstabs-1">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td>
+ <table cellpadding="20" cellspacing="0">
+ <tr>
+ <td class="fs14 fwb ffl b1 cw cbrb" align="left" width="180">Statistic</td>
- <option value="12">
- 13
- </option>
+ <td class="fs14 fwb ffl b1 cw cbrb" align="right" width="60">Value</td>
+ </tr>
- <option value="13">
- 14
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" align="left">N of Samples</td>
- <option value="14">
- 15
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">32</td>
+ </tr>
- <option value="15">
- 16
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Mean</td>
- <option value="16">
- 17
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">6.176</td>
+ </tr>
- <option value="17">
- 18
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Median</td>
- <option value="18">
- 19
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">6.170</td>
+ </tr>
- <option value="19">
- X
- </option>
- </select></td>
- </tr>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Error (SE)</td>
- <tr>
- <td><span class="ffl fwb fs12">Mapping Scale:</span></td>
+ <td class="fs13 b1 cbw c222" nowrap="yes">0.027</td>
+ </tr>
- <td><select name="scale2" size="1" onchange=
- "checkUncheck(window.document.dataInput.scale2.value, window.document.dataInput.permCheck2, window.document.dataInput.bootCheck2)">
- <option value="physic">
- Megabase
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Standard Deviation (SD)</td>
- <option value="morgan">
- Centimorgan
- </option>
- </select></td>
- </tr>
-
- <tr>
- <td><span class="ffl fwb fs12">Control Locus:</span></td>
-
- <td><input type="text" name="controlLocus" class="controlLocus"></td>
- </tr>
- </table><br>
- <input type="checkbox" name="permCheck2" class="checkbox" checked>Permutation Test (n=2000)<br>
- <input type="checkbox" name="bootCheck2" class="checkbox">Bootstrap Test (n=2000)<br>
- <input type="checkbox" name="parentsf14regression3" class="checkbox">Use Parents<br>
- <br>
- <input type="button" name="composite" class="btn" value=" Compute "><br>
- <br>
- </td>
- </tr>
-
- <tr>
- <td valign="top"><span><a href="/glossary.html#Composite" target="_blank">Composite Interval Mapping</a> allows you to control
- for a single marker as<br>
- a cofactor. To find a control marker, run the <strong>Marker Regression</strong> function.</span><br></td>
- </tr>
- </table>
- </div>
-
- <div id="mappingtabs-4">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td class="fs12 fwn" nowrap="on">
- <table cellpadding="2" cellspacing="0" width="232px">
- <tr>
- <td><span class="ffl fwb fs12"><strong>Sort by:</strong></span></td>
-
- <td><select name="graphSort" size="1">
- <option value="0">
- LRS Full
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">0.150</td>
+ </tr>
- <option value="1">
- LRS Interact
- </option>
- </select></td>
- </tr>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Minimum</td>
- <tr>
- <td><span class="ffl fwb fs12"><strong>Return:</strong></span></td>
+ <td class="fs13 b1 cbw c222" nowrap="yes">5.906</td>
+ </tr>
- <td><select name="pairScanReturn" size="1">
- <option value="50">
- top 50
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Maximum</td>
- <option value="100">
- top 100
- </option>
+ <td class="fs13 b1 cbw c222" nowrap="yes">6.485</td>
+ </tr>
- <option value="200">
- top 200
- </option>
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left">Range (log2)</td>
+
+ <td class="fs13 b1 cbw c222" nowrap="yes">0.579</td>
+ </tr>
+
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span>Range (fold)</span></td>
+
+ <td class="fs13 b1 cbw c222" nowrap="yes">1.49</td>
+ </tr>
+
+ <tr align="right">
+ <td class="fs13 b1 cbw c222" nowrap="yes" align="left"><span><a href="/glossary.html#Interquartile" target="_blank" class=
+ "non_bold">Interquartile Range</a></span></td>
+
+ <td class="fs13 b1 cbw c222" nowrap="yes">1.15</td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
+ </div>
+
+ <div id="statstabs-5">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td><img src="/image/nP_swDAFlJy.gif" alt="nP_swDAFlJy.gif" border="0"></td>
+ </tr>
+
+ <tr>
+ <td><br>
+ <br>
+ This plot evaluates whether data are normally distributed. Different symbols represent different groups.<br>
+ <br>
+ More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot" target="_blank">Normal Probability Plots</a> and more
+ about interpreting these plots from the <a href="/glossary.html#normal_probability" target="_blank">glossary</a></td>
+ </tr>
+ </table>
+ </div>
+
+ <div id="statstabs-2">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td align="left">
+ <img src="/image/Box_6sQJ8xhK.gif" alt="Box_6sQJ8xhK.gif" border="0">
+
+ <p><span>More about <a href="http://davidmlane.com/hyperstat/A37797.html" target="_blank" class="fs13">Box Plots</a></span></p>
+ </td>
+ </tr>
+ </table>
+ </div>
+
+ <div id="statstabs-3">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td><img src="/image/Bar_QMWE2VEp.gif" alt="Bar_QMWE2VEp.gif" border="0"></td>
+ </tr>
+ </table>
+ </div>
+
+ <div id="statstabs-4">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td><img src="/image/Bar_X07QmgsX.gif" alt="Bar_X07QmgsX.gif" border="0"></td>
+ </tr>
+ </table>
+ </div>
+ </div>
+ </td>
+ </tr>
+ </table>
+ #}
+
+ <p class="sectionheader" id="title3" style="border-radius: 5px;">&nbsp;&nbsp;Calculate Correlations</p>
+
+ <p id="sectionbody3"></p>
+
+ <table class="target4" cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td>
+ <div class="ui-tabs" id="corr_tabs">
+ <div id="corrtabs-1">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td>
+ <input type="hidden" name="orderBy" value="2">
+
+ <table cellpadding="2" cellspacing="0" width="619px">
+ <tr>
+ <td><span class="ff1 fwb fs12">Method:</span></td>
+ <td colspan="3">
+ <select name="corr_method" size="1">
+ <option value="sample">Sample r</option>
+ <option value="lit">Literature r</option>
+ <option value="tissue">Tissue r</option>
+ </select>
+ </td>
+ </tr>
+ <tr>
+ <td><span class="ffl fwb fs12">Database:</span></td>
+ <td colspan="3">
+ <select name="corr_dataset" size="1">
+ {% for tissue in corr_tools.dataset_menu %}
+ {% if tissue.tissue %}
+ <optgroup label="{{ tissue.tissue }} ------">
+ {% endif %}
+ {% for dataset in tissue.datasets %}
+ <option value="{{ dataset[1] }}"
+ {% if corr_tools.dataset_menu_selected == dataset[1] %}
+ selected
+ {% endif %}>
+ {{ dataset[0] }}
+ </option>
+ {% endfor %}
+ {% if tissue.tissue %}
+ </optgroup>
+ {% endif %}
+ {% endfor %}
+ </select>
+ </td>
+ </tr>
+
+
+ <tr>
+ <td><span class="ffl fwb fs12">Return:</span></td>
+
+ <td><select name="corr_return_results" size="1">
+ {% for return_result in corr_tools.return_results_menu %}
+ <option value="{{ return_result }}"
+ {% if corr_tools.return_results_menu_selected == return_result %}
+ selected
+ {% endif %}>
+ Top {{ return_result }}
+ </option>
+ {% endfor %}
+ </select></td>
+ </tr>
+
+
+ <tr class="mdp1">
+ <td><span class="ffl fwb fs12">Samples:</span></td>
+ <td>
+ <select name="corr_samples_group" size="1">
+ {% for group, pretty_group in sample_group_types.items() %}
+ <option value="{{ group }}">
+ {{ pretty_group }}
+ </option>
+ {% endfor %}
+ </select>
+ </td>
+ </tr>
+
+ </table>
+ <br>
+ <div id="corr_sample_method_options">
+ Pearson <input type="radio" name="corr_sample_method" value="pearson" checked>
+ &nbsp;&nbsp;&nbsp;
+ Spearman Rank <input type="radio" name="corr_sample_method" value="spearman">
+ </div>
+ <br>
+
+ <input type="submit" name="corr_compute" id="corr_compute" class="btn" value="Compute"><br><br>
+
+ <span id="sample_r_desc" class="correlation_desc fs12">
+ The <a href="/correlationAnnotation.html#sample_r" target="_blank">Sample Correlation</a>
+ is computed
+ between trait data and any<br>
+ other traits in the sample database selected above. Use
+ <a href="/glossary.html#Correlations" target="_blank">Spearman
+ Rank</a><br>
+ when the sample size is small (&lt;20) or when there are influential outliers.
+ </span>
+ <SPAN id="lit_r_desc" style="display: none;" class="correlation_desc fs12">
+ The <A HREF="/correlationAnnotation.html" TARGET="_blank">Literature Correlation</A>
+ (Lit r) between
+ this gene and all other genes is computed<BR>
+ using the <A HREF="https://grits.eecs.utk.edu/sgo/sgo.html" TARGET="_blank">
+ Semantic Gene Organizer</A>
+ and human, rat, and mouse data from PubMed. <BR>
+ Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<BR><BR>
+ <A HREF="/glossary.html#Literature" TARGET="_blank">More on using Lit r</A>
+ </SPAN>
+ <SPAN id="tissue_r_desc" style="display: none;" class="correlation_desc fs12">
+ The <A HREF="/webqtl/main.py?FormID=tissueCorrelation" TARGET="_blank">Tissue Correlation</A>
+ (Tissue r)
+ estimates the similarity of expression of two genes<BR>
+ or transcripts across different cells, tissues, or organs
+ (<A HREF="/correlationAnnotation.html#tissue_r" TARGET="_blank">glossary</A>).
+ Tissue correlations<BR>
+ are generated by analyzing expression in multiple samples usually taken from single cases.<BR>
+ <STRONG>Pearson</STRONG> and <STRONG>Spearman Rank</STRONG> correlations have been
+ computed for all pairs of genes<BR> using data from mouse samples.<BR>
+ </SPAN>
+
+ <br>
+ </td>
+ </tr>
+ </table>
+ </div>
+ </div>
+ </td>
+ </tr>
+ </table>
+
+ <p class="sectionheader" id="title4" style="border-radius: 5px;">&nbsp;&nbsp;Mapping Tools</p>
+
+ <p id="sectionbody4"></p><script language="Javascript" type="text/javascript">
+ <!--
+
+ //$(function() { $("#mapping_tabs").tabs(); });
+
+ //-->
+ </script>
+
+ <table class="target2" cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td>
+ <div class="ui-tabs" id="mapping_tabs">
+ <ul>
+ <li><a href="#mappingtabs-1">Interval</a></li>
+
+ <li><a href="#mappingtabs-2">Marker Regression</a></li>
+
+ <li><a href="#mappingtabs-3">Composite</a></li>
+
+ <li><a href="#mappingtabs-4">Pair-Scan</a></li>
+ </ul>
+
+ <div id="mappingtabs-1">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td class="fs12 fwn" nowrap="on" valign="top">
+ <table cellpadding="2" cellspacing="0" width="263px">
+ <tr>
+ <td><span class="ffl fwb fs12">Chromosome:</span></td>
+
+ <td colspan="3"><select name="chromosomes1" size="1">
+ <option value="-1">
+ All
+ </option>
+
+ <option value="0">
+ 1
+ </option>
+
+ <option value="1">
+ 2
+ </option>
+
+ <option value="2">
+ 3
+ </option>
+
+ <option value="3">
+ 4
+ </option>
+
+ <option value="4">
+ 5
+ </option>
+
+ <option value="5">
+ 6
+ </option>
+
+ <option value="6">
+ 7
+ </option>
+
+ <option value="7">
+ 8
+ </option>
+
+ <option value="8">
+ 9
+ </option>
+
+ <option value="9">
+ 10
+ </option>
+
+ <option value="10">
+ 11
+ </option>
+
+ <option value="11">
+ 12
+ </option>
+
+ <option value="12">
+ 13
+ </option>
+
+ <option value="13">
+ 14
+ </option>
+
+ <option value="14">
+ 15
+ </option>
+
+ <option value="15">
+ 16
+ </option>
+
+ <option value="16">
+ 17
+ </option>
+
+ <option value="17">
+ 18
+ </option>
+
+ <option value="18">
+ 19
+ </option>
+
+ <option value="19">
+ X
+ </option>
+ </select></td>
+ </tr>
+
+ <tr>
+ <td><span class="ffl fwb fs12">Mapping Scale:</span></td>
+
+ <td><select name="scale1" size="1" onchange=
+ "checkUncheck(window.document.dataInput.scale1.value, window.document.dataInput.permCheck1, window.document.dataInput.bootCheck1)">
+ <option value="physic">
+ Megabase
+ </option>
+
+ <option value="morgan">
+ Centimorgan
+ </option>
+ </select></td>
+ </tr>
+ </table><br>
+ <input type="checkbox" name="permCheck1" class="checkbox" checked>Permutation Test (n=2000)<br>
+ <input type="checkbox" name="bootCheck1" class="checkbox">Bootstrap Test (n=2000)<br>
+ <input type="checkbox" name="parentsf14regression1" class="checkbox">Use Parents<br>
+ <input type="checkbox" name="applyVarianceSE1" class="checkbox">Use Weighted<br>
+ <br>
+ <input type="button" name="interval" class="btn" value=" Compute "><br>
+ <br>
+ </td>
+ </tr>
+
+ <tr>
+ <td valign="top"><span class="fs12"><a href="/glossary.html#intmap" target="_blank">Interval Mapping</a> computes linkage maps
+ for the entire genome or single<br>
+ chromosomes. The <a href="/glossary.html#permutation" target="_blank">Permutation Test</a> estimates suggestive and
+ significant<br>
+ linkage scores. The <a href="/glossary.html#bootstrap" target="_blank">Bootstrap Test</a> estimates the precision of the QTL
+ location.</span><br></td>
+ </tr>
+ </table>
+ </div>
+
+ <div id="mappingtabs-2">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td class="fs12 fwn" nowrap="on" valign="top">
+ <table cellpadding="2" cellspacing="0" width="263px">
+ <tr>
+ <td><span class="ffl fwb fs12"><strong>Display LRS greater than:</strong></span></td>
+
+ <td><input type="text" name="suggestive" size="5" maxlength="8"></td>
+ </tr>
+
+ <tr>
+ <td><input type="checkbox" name="displayAllLRS" class="checkbox"> <span class="ffl fs12">Display all LRS</span></td>
+ </tr>
+
+ <tr>
+ <td><input type="checkbox" name="parentsf14regression2" class="checkbox"> <span class="ffl fs12">Use Parents</span></td>
+ </tr>
+
+ <tr>
+ <td><input type="checkbox" name="applyVarianceSE2" class="checkbox"> <span class="ffl fs12">Use Weighted</span></td>
+ </tr>
+ </table><br>
+ <input type="button" name="marker" class="btn" value=" Compute "><br>
+ <br>
+ </td>
+ </tr>
+
+ <tr>
+ <td valign="top"><span class="fs12"><a href="/glossary.html#" target="_blank">Marker regression</a> computes and displays LRS
+ values for individual markers.<br>
+ This function also lists additive effects (phenotype units per allele) and<br>
+ dominance deviations for some datasets.<br></span><br></td>
+ </tr>
+ </table>
+ </div>
+
+ <div id="mappingtabs-3">
+ <table cellpadding="3" cellspacing="0" width="100%">
+ <tr>
+ <td class="fs12 fwn" nowrap="on" valign="top">
+ <table cellpadding="2" cellspacing="0" width="325px">
+ <tr>
+ <td><span class="ffl fwb fs12">Chromosome:</span></td>
+
+ <td colspan="3"><select name="chromosomes2" size="1">
+ <option value="-1">
+ All
+ </option>
+
+ <option value="0">
+ 1
+ </option>
+
+ <option value="1">
+ 2
+ </option>
+
+ <option value="2">
+ 3
+ </option>
+
+ <option value="3">
+ 4
+ </option>
+
+ <option value="4">
+ 5
+ </option>
+
+ <option value="5">
+ 6
+ </option>
+
+ <option value="6">
+ 7
+ </option>
+
+ <option value="7">
+ 8
+ </option>
+
+ <option value="8">
+ 9
+ </option>
+
+ <option value="9">
+ 10
+ </option>
+
+ <option value="10">
+ 11
+ </option>
+
+ <option value="11">
+ 12
+ </option>
+
+ <option value="12">
+ 13
+ </option>
+
+ <option value="13">
+ 14
+ </option>
+
+ <option value="14">
+ 15
+ </option>
+
+ <option value="15">
+ 16
+ </option>
+
+ <option value="16">
+ 17
+ </option>
+
+ <option value="17">
+ 18
+ </option>
+
+ <option value="18">
+ 19
+ </option>
+
+ <option value="19">
+ X
+ </option>
+ </select></td>
+ </tr>
+
+ <tr>
+ <td><span class="ffl fwb fs12">Mapping Scale:</span></td>
+
+ <td><select name="scale2" size="1" onchange=
+ "checkUncheck(window.document.dataInput.scale2.value, window.document.dataInput.permCheck2, window.document.dataInput.bootCheck2)">
+ <option value="physic">
+ Megabase
+ </option>
+
+ <option value="morgan">
+ Centimorgan
+ </option>
+ </select></td>
+ </tr>
+
+ <tr>
+ <td><span class="ffl fwb fs12">Control Locus:</span></td>
+
+ <td><input type="text" name="controlLocus" class="controlLocus"></td>
+ </tr>
+ </table><br>
+ <input type="checkbox" name="permCheck2" class="checkbox" checked>Permutation Test (n=2000)<br>
+ <input type="checkbox" name="bootCheck2" class="checkbox">Bootstrap Test (n=2000)<br>
+ <input type="checkbox" name="parentsf14regression3" class="checkbox">Use Parents<br>
+ <br>
+ <input type="button" name="composite" class="btn" value=" Compute "><br>
+ <br>
+ </td>
+ </tr>
+
+ <tr>
+ <td valign="top"><span><a href="/glossary.html#Composite" target="_blank">Composite Interval Mapping</a> allows you to control
+ for a single marker as<br>
+ a cofactor. To find a control marker, run the <strong>Marker Regression</strong> function.</span><br></td>
+ </tr>
+ </table>
+ </div>
+
+ <div id="mappingtabs-4">
+ <table cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td class="fs12 fwn" nowrap="on">
+ <table cellpadding="2" cellspacing="0" width="232px">
+ <tr>
+ <td><span class="ffl fwb fs12"><strong>Sort by:</strong></span></td>
+
+ <td><select name="graphSort" size="1">
+ <option value="0">
+ LRS Full
+ </option>
+
+ <option value="1">
+ LRS Interact
+ </option>
+ </select></td>
+ </tr>
+
+ <tr>
+ <td><span class="ffl fwb fs12"><strong>Return:</strong></span></td>
+
+ <td><select name="pairScanReturn" size="1">
+ <option value="50">
+ top 50
+ </option>
+
+ <option value="100">
+ top 100
+ </option>
+
+ <option value="200">
+ top 200
+ </option>
+
+ <option value="500">
+ top 500
+ </option>
+ </select></td>
+ </tr>
+ </table><br>
+ <input type="checkbox" name="directPermuCheckbox" class="checkbox" checked><span class="ffl fs12">Permutation Test
+ (n=500)</span><br>
+ <br>
+ <input type="button" class="btn" value=" Compute " onclick="dataEditingFunc(this.form,'directPlot');"><br>
+ <br>
+ </td>
+ </tr>
+
+ <tr>
+ <td valign="top"><span><a href="/glossary.html#Pair_Scan" target="_blank">Pair-Scan</a> searches for pairs of chromosomal regions
+ that are<br>
+ involved in two-locus epistatic interactions.</span><br></td>
+ </tr>
+ </table>
+ </div>
+ </div>
+ </td>
+ </tr>
+ </table>
+
+ <p class="sectionheader" id="title5" style="border-radius: 5px;">&nbsp;&nbsp;Review and Edit Data</p>
+
+ <table id="stats_table" class="one-column-emphasis" />
+
+ <p id="sectionbody5"></p>
- <option value="500">
- top 500
+ <table class="target5" id="value_table" cellpadding="0" cellspacing="0" width="100%">
+ <tr>
+ <td>
+ <div>
+ <div class="well">
+ <fieldset id="showHideOptions">
+ <legend>Block samples</legend>
+ <p>Edit or delete values in the Trait Data boxes, and use the
+ <strong>Reset</strong> option as
+ needed.
+ </p>
+
+
+ <div id="blockMenuSpan" class="input-append">
+ <label for="remove_samples_field">Block samples by index:</label>
+
+
+ <input type="text" id="remove_samples_field">
+ <select id="block_group" size="1">
+ <option value="primary">
+ {{ sample_group_types['primary_only'] }}
+ </option>
+ <option value="other">
+ {{ sample_group_types['other_only'] }}
</option>
- </select></td>
- </tr>
- </table><br>
- <input type="checkbox" name="directPermuCheckbox" class="checkbox" checked><span class="ffl fs12">Permutation Test
- (n=500)</span><br>
+ </select>
+ <input type="button" id="block_by_index" class="btn" value="Block">
+ </div>
+ <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
+ Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
+ </div>
+
<br>
- <input type="button" class="btn" value=" Compute " onclick="dataEditingFunc(this.form,'directPlot');"><br>
+
+ {% if sample_groups[0].attributes %}
+ <div class="input-append">
+ <label for="exclude_menu">Block samples by group:</label>
+ <select id="exclude_menu" size=1>
+ {% for attribute in sample_groups[0].attributes %}
+ <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
+ {{ sample_groups[0].attributes[attribute].name }}</option>
+ {% endfor %}
+ </select>
+ <select id="attribute_values" size=1>
+ </select>
+ <input type="button" id="exclude_group" class="btn" value="Block">
+ </div>
+ {% endif %}
<br>
- </td>
- </tr>
-
- <tr>
- <td valign="top"><span><a href="/glossary.html#Pair_Scan" target="_blank">Pair-Scan</a> searches for pairs of chromosomal regions
- that are<br>
- involved in two-locus epistatic interactions.</span><br></td>
- </tr>
- </table>
- </div>
- </div>
- </td>
- </tr>
- </table>
-
- <p class="sectionheader" id="title5" style="border-radius: 5px;">&nbsp;&nbsp;Review and Edit Data</p>
-
- <table id="stats_table" class="one-column-emphasis" />
-
- <p id="sectionbody5"></p>
-
- <table class="target5" id="value_table" cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td>
- <div>
- <div class="well">
- <fieldset id="showHideOptions">
- <legend>Block samples</legend>
- <p>Edit or delete values in the Trait Data boxes, and use the
- <strong>Reset</strong> option as
- needed.
- </p>
-
-
- <div id="blockMenuSpan" class="input-append">
- <label for="remove_samples_field">Block samples by index:</label>
-
-
- <input type="text" id="remove_samples_field">
- <select id="block_group" size="1">
- <option value="primary">
- {{ sample_group_types['primary_only'] }}
- </option>
- <option value="other">
- {{ sample_group_types['other_only'] }}
- </option>
- </select>
- <input type="button" id="block_by_index" class="btn" value="Block">
+ <div>
+ <input type="button" id="hide_no_value" class="btn" value="Hide No Value">
+ <input type="button" id="block_outliers" class="btn" value="Block Outliers">
+ <input type="button" id="reset" class="btn btn-inverse" value="Reset">
+ <span class="input-append">
+ <input type="button" id="export" class="btn" value="Export">
+ <select id="export_format" class="select optional span2">
+ <option value="excel">Excel</option>
+ <option value="csv">CSV</option>
+ </select>
+ </span>
+ </div>
+ </fieldset>
+ <br>
+ <div>
+ <p>Outliers highlighted in
+ <strong style="background-color:yellow;">yellow</strong>
+ can be hidden using
+ the <strong>Hide Outliers</strong> button.
+ </p>
+
+ <p>Samples with no value (x) can be hidden by clicking
+ <strong>Hide No Value</strong> button.
+ </p>
</div>
- <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
- Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
</div>
-
<br>
- {% if sample_groups[0].attributes %}
- <div class="input-append">
- <label for="exclude_menu">Block samples by group:</label>
- <select id="exclude_menu" size=1>
- {% for attribute in sample_groups[0].attributes %}
- <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
- {{ sample_groups[0].attributes[attribute].name }}</option>
+
+
+ <div style="width:80%;margin:0;padding:0;border:none;">
+ {% for sample_type in sample_groups %}
+ <div style="float:left;width:50%;">
+ <h2>{{ sample_type.header }}</h2>
+
+ <div id="{{ sample_type.sample_group_type }}">
+ <table class="table table-hover not_tablesorter" {# Todo: Turn tablesorter back on #}
+ id="{{ 'sortable%i' % (loop.index) }}"
+ cellpadding="0" cellspacing="0">
+ <tr>
+ <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="60">Index</th>
+
+ <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="100">Sample</th>
+
+ <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="70">Value</th>
+ {% if sample_type.se_exists() %}
+ <th class="fs13 fwb ff1 b1 cw cbrb" width="20">&nbsp;</th>
+
+ <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="80">SE</th>
+ {% endif %}
+
+ {% for attribute in sample_type.attributes|sort() %}
+ <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="60">
+ {{ sample_type.attributes[attribute].name }}
+ </th>
+ {% endfor %}
+ </tr>
+
+ {% for sample in sample_type.sample_list %}
+ <tr class="{{ sample.class_outlier }} value_se" id="{{ sample.this_id }}">
+ <td class="std_cell column_name-Index" align="right" width="45">
+ {{ loop.index }}
+ <input type="checkbox" name="selectCheck"
+ class="checkbox edit_sample_checkbox"
+ value="{{ sample.name }}" checked="checked">
+ </td>
+
+ <td class="std_cell column_name-Sample" align="right" width="100">
+ <span class="fs14 fwn ffl edit_sample_sample_name">
+ {{ sample.name }}
+ </span>
+ </td>
+
+ {# Todo: Add IDs #}
+ <td class="std_cell column_name-Value" align="right" width="70">
+ <input type="text" data-value="{{ sample.display_value }}" name="{{ sample.name }}"
+ class="trait_value_input edit_sample_value"
+ value="{{ sample.display_value }}" size="8" maxlength="8"
+ style="text-align:right; background-color:#FFFFFF;">
+ </td>
+
+ {% if sample_type.se_exists() %}
+ <td class="std_cell" align="center" width="20">
+ ±
+ </td>
+
+ {# Todo: Add IDs #}
+ <td class="std_cell column_name-SE" align="right" width="80">
+ <input type="text" data-value="{{ sample.display_variance }}" name=""{{ 'V' + sample.name}}"
+ class="trait_value_input edit_sample_se"
+ value="{{ sample.display_variance }}"
+ size="8" maxlength="8" style="text-align:right">
+ </td>
+ {% endif %}
+
+ {# Loop through each attribute type and input value #}
+ {% for attribute in sample_type.attributes|sort() %}
+ <td class="std_cell column_name-{{ sample_type.attributes[attribute].name.replace(' ', '_') }}"
+ align="right" width="80">
+ {{ sample.extra_attributes[sample_type.attributes[attribute].name] }}
+ </td>
{% endfor %}
- </select>
- <select id="attribute_values" size=1>
- </select>
- <input type="button" id="exclude_group" class="btn" value="Block">
+ </tr>
+ {% endfor %}
+
+ </table>
+ </div>
</div>
- {% endif %}
- <br>
- <div>
- <input type="button" id="hide_no_value" class="btn" value="Hide No Value">
- <input type="button" id="block_outliers" class="btn" value="Block Outliers">
- <input type="button" id="reset" class="btn btn-inverse" value="Reset">
- <span class="input-append">
- <input type="button" id="export" class="btn" value="Export">
- <select id="export_format" class="select optional span2">
- <option value="excel">Excel</option>
- <option value="csv">CSV</option>
- </select>
- </span>
- </div>
- </fieldset>
- <br>
- <div>
- <p>Outliers highlighted in
- <strong style="background-color:yellow;">yellow</strong>
- can be hidden using
- the <strong>Hide Outliers</strong> button.
- </p>
-
- <p>Samples with no value (x) can be hidden by clicking
- <strong>Hide No Value</strong> button.
- </p>
- </div>
- </div>
- <br>
-
-
-
- <div style="width:80%;margin:0;padding:0;border:none;">
- {% for sample_type in sample_groups %}
- <div style="float:left;width:50%;">
- <h2>{{ sample_type.header }}</h2>
-
- <div id="{{ sample_type.sample_group_type }}">
- <table class="table table-hover not_tablesorter" {# Todo: Turn tablesorter back on #}
- id="{{ 'sortable%i' % (loop.index) }}"
- cellpadding="0" cellspacing="0">
- <tr>
- <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="60">Index</th>
-
- <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="100">Sample</th>
-
- <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="70">Value</th>
- {% if sample_type.se_exists() %}
- <th class="fs13 fwb ff1 b1 cw cbrb" width="20">&nbsp;</th>
-
- <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="80">SE</th>
- {% endif %}
-
- {% for attribute in sample_type.attributes|sort() %}
- <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="60">
- {{ sample_type.attributes[attribute].name }}
- </th>
- {% endfor %}
- </tr>
-
- {% for sample in sample_type.sample_list %}
- <tr class="{{ sample.class_outlier }} value_se" id="{{ sample.this_id }}">
- <td class="std_cell column_name-Index" align="right" width="45">
- {{ loop.index }}
- <input type="checkbox" name="selectCheck"
- class="checkbox edit_sample_checkbox"
- value="{{ sample.name }}" checked="checked">
- </td>
-
- <td class="std_cell column_name-Sample" align="right" width="100">
- <span class="fs14 fwn ffl edit_sample_sample_name">
- {{ sample.name }}
- </span>
- </td>
-
- {# Todo: Add IDs #}
- <td class="std_cell column_name-Value" align="right" width="70">
- <input type="text" data-value="{{ sample.display_value }}" name="{{ sample.name }}"
- class="trait_value_input edit_sample_value"
- value="{{ sample.display_value }}" size="8" maxlength="8"
- style="text-align:right; background-color:#FFFFFF;">
- </td>
-
- {% if sample_type.se_exists() %}
- <td class="std_cell" align="center" width="20">
- ±
- </td>
-
- {# Todo: Add IDs #}
- <td class="std_cell column_name-SE" align="right" width="80">
- <input type="text" data-value="{{ sample.display_variance }}" name=""{{ 'V' + sample.name}}"
- class="trait_value_input edit_sample_se"
- value="{{ sample.display_variance }}"
- size="8" maxlength="8" style="text-align:right">
- </td>
- {% endif %}
-
- {# Loop through each attribute type and input value #}
- {% for attribute in sample_type.attributes|sort() %}
- <td class="std_cell column_name-{{ sample_type.attributes[attribute].name.replace(' ', '_') }}"
- align="right" width="80">
- {{ sample.extra_attributes[sample_type.attributes[attribute].name] }}
- </td>
- {% endfor %}
- </tr>
{% endfor %}
-
- </table>
- </div>
- </div>
- {% endfor %}
- </div>
- </div>
- </td>
- </tr>
- </table>
- <input type="hidden" name="Default_Name">
- </form>
- </td>
- </tr>
- </table>
- </td>
- </tr>
-
+ </div>
+ </div>
+ </td>
+ </tr>
+ </table>
+ <input type="hidden" name="Default_Name">
+ </form>
+ </td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </div>
<script>
js_data = {{ js_data | safe }}
</script>
@@ -1382,16 +1428,16 @@
<script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>-->
<script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script>
<script type="text/javascript" src="/static/new/packages/ValidationPlugin/dist/jquery.validate.min.js"></script>
-
+
<script type="text/javascript" src="/static/new/javascript/stats.js"></script>
<script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
<script type="text/javascript" src="/static/new/js_external/json2.js"></script>
<script type="text/javascript" src="/static/new/javascript/validation.js"></script>
-
+
<!-- End of body -->
-
-
-
-
- {% endblock %}
+
+
+
+
+{% endblock %}
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 22:24:35 +0000