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authorLei Yan2016-02-25 16:42:15 +0000
committerLei Yan2016-02-25 16:42:15 +0000
commite55f38a72d47fbdf5f652a08e8da1db78f1dcdb5 (patch)
tree68161b76858cf72f7a7b5576de6384042e214d8e /wqflask/wqflask/templates
parent7263c52a7d903a2dbdd5d05411821ec960961b4d (diff)
parentece60a2d25ed71980121ac1c1854c3ab3514f453 (diff)
downloadgenenetwork2-e55f38a72d47fbdf5f652a08e8da1db78f1dcdb5.tar.gz
Merge /home/zas1024/gene
Diffstat (limited to 'wqflask/wqflask/templates')
-rwxr-xr-xwqflask/wqflask/templates/all_results.html134
-rwxr-xr-xwqflask/wqflask/templates/base.html8
-rwxr-xr-xwqflask/wqflask/templates/correlation_page.html20
-rwxr-xr-xwqflask/wqflask/templates/index_page.html7
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html337
-rw-r--r--wqflask/wqflask/templates/marker_regression_old.html106
-rwxr-xr-xwqflask/wqflask/templates/new_security/login_user.html1
-rwxr-xr-xwqflask/wqflask/templates/quick_search.html300
-rwxr-xr-xwqflask/wqflask/templates/search_result_page.html29
-rwxr-xr-xwqflask/wqflask/templates/show_trait.html15
-rwxr-xr-xwqflask/wqflask/templates/show_trait_calculate_correlations.html2
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html20
-rwxr-xr-xwqflask/wqflask/templates/show_trait_statistics.html578
-rwxr-xr-xwqflask/wqflask/templates/show_trait_statistics_new.html155
-rwxr-xr-xwqflask/wqflask/templates/whats_new.html18
15 files changed, 366 insertions, 1364 deletions
diff --git a/wqflask/wqflask/templates/all_results.html b/wqflask/wqflask/templates/all_results.html
deleted file mode 100755
index a42e42d8..00000000
--- a/wqflask/wqflask/templates/all_results.html
+++ /dev/null
@@ -1,134 +0,0 @@
- <ul class="nav nav-tabs">
- {% for species in species_groups %}
- <li> <a href="#tab{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
- {% endfor %}
- </ul>
- <div class="tab-content">
- {% for species in species_groups %}
- <div class="tab-pane active" id="tab{{ loop.index }}">
- <div class="tabbable tabs-left">
- <ul class="nav nav-tabs">
- {% if species_groups[species]['phenotype'] %}
- <li class="active"> <a href="#tab{{ loop.index }}_1" data-toggle="tab">Phenotype</a></li>
- {% endif %}
- {% if species_groups[species]['mrna_assay'] %}
- <li> <a href="#tab{{ loop.index }}_2" data-toggle="tab">mRNA Assay</a></li>
- {% endif %}
- {% if species_groups[species]['genotype'] %}
- <li> <a href="#tab{{ loop.index }}_3" data-toggle="tab">Genotype</a></li>
- {% endif %}
- </ul>
- <div class="tab-content">
- {% if species_groups[species]['phenotype'] %}
- <div class="tab-pane active" id="tab{{ loop.index }}_1">
- <table id="pheno_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <th>Id</th>
- <th>Species</th>
- <th>Group</th>
- <th>Description</th>
- <th>LRS</th>
- <th>Year</th>
- <th>Authors</th>
- </tr>
- </thead>
- <tbody>
- {% for result in results.phenotype %}
- {% if result.result_fields['species'] == species %}
- <tr>
- <td>{{ result.result_fields['phenotype_id'] }}</td>
- <td>{{ result.result_fields['species'] }}</td>
- <td>{{ result.result_fields['group_name'] }}</td>
- <td>{{ result.result_fields['description'] }}</td>
- <td>{{ result.result_fields['lrs'] }}</td>
- <td>
- <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract">
- {{ result.result_fields['year'] }}
- </a>
- </td>
- <td>{{ result.result_fields['authors'] }}</td>
- </tr>
- {% endif %}
- {% endfor %}
- </tbody>
- </table>
- </div>
- {% endif %}
- {% if species_groups[species]['mrna_assay'] %}
- <div class="tab-pane" id="tab{{ loop.index }}_2">
- <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <th>Record ID</th>
- <th>Species</th>
- <th>Group</th>
- <th>Data Set</th>
- <th>Symbol</th>
- <th>Description</th>
- <th>Location</th>
- <th>Mean Expr</th>
- <th>Max LRS</th>
- </tr>
- </thead>
- <tbody>
- {% for result in results.mrna_assay %}
- {% if result.result_fields['species'] == species %}
- <tr>
- <td>
- <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
- {{ result.result_fields['name'] }}
- </a>
- </td>
- <td>{{ result.result_fields['species'] }}</td>
- <td>{{ result.result_fields['group_name'] }}</td>
- <td>{{ result.result_fields['dataset_name'] }}</td>
- <td>{{ result.result_fields['symbol'] }}</td>
- <td>{{ result.result_fields['description'] }}</td>
- <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
- <td>{{ result.result_fields['mean'] }}</td>
- <td>{{ result.result_fields['lrs'] }}</td>
- </tr>
- {% endif %}
- {% endfor %}
- </tbody>
- </table>
- </div>
- {% endif %}
- {% if species_groups[species]['genotype'] %}
- <div class="tab-pane" id="tab{{ loop.index }}_3">
- <table id="geno_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <th>Marker</th>
- <th>Species</th>
- <th>Group</th>
- <th>Data Set</th>
- <th>Location</th>
- </tr>
- </thead>
- <tbody>
- {% for result in results.genotype %}
- {% if result.result_fields['species'] == species %}
- <tr>
- <td>
- <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}">
- {{ result.result_fields['marker_name'] }}
- </a>
- </td>
- <td>{{ result.result_fields['species'] }}</td>
- <td>{{ result.result_fields['group_name'] }}</td>
- <td>{{ result.result_fields['dataset_name'] }}</td>
- <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td>
- </tr>
- {% endif %}
- {% endfor %}
- </tbody>
- </table>
- </div>
- {% endif %}
- </div>
- </div>
- </div>
- {% endfor %}
- </div> \ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 4d44642b..f25bf9f7 100755
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -1,7 +1,6 @@
{% from "base_macro.html" import header, flash_me, timeago %}
<!DOCTYPE HTML>
-<html lang="en">
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html lang="en" xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
@@ -35,6 +34,9 @@
<div>
<ul class="nav navbar-nav">
<li class="">
+ <a href="/intro">Intro</a>
+ </li>
+ <li class="">
<a href="/">Search</a>
</li>
<li class="">
@@ -71,7 +73,7 @@
</li>
<li style="margin-left: 20px;">
<a href="http://www.genenetwork.org" style="font-weight: bold;" >Use GeneNetwork 1</a>
- </li
+ </li>
</ul>
</div>
</div>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 9dddc7ce..efc94c42 100755
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -5,6 +5,7 @@
<link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
<link href="//cdn.datatables.net/fixedheader/2.1.2/css/dataTables.fixedHeader.css" rel="stylesheet">
<link href="//cdn.datatables.net/fixedcolumns/3.0.4/css/dataTables.fixedColumns.css" rel="stylesheet">
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
{% endblock %}
{% block content %}
@@ -155,6 +156,10 @@
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
+ <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
+ <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script>
+ <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
@@ -245,7 +250,10 @@
{ "type": "natural" },
{ "type": "natural" }
],
- "sDom": "RZtir",
+ "buttons": [
+ 'csvHtml5'
+ ],
+ "sDom": "RZBtir",
"iDisplayLength": -1,
"bDeferRender": true,
"bSortClasses": false,
@@ -273,7 +281,10 @@
{ "type": "natural" },
{ "type": "natural" }
],
- "sDom": "RZtir",
+ "buttons": [
+ 'csvHtml5'
+ ],
+ "sDom": "RZBtir",
"iDisplayLength": -1,
"autoWidth": true,
"bLengthChange": true,
@@ -297,7 +308,10 @@
{ "type": "natural" },
{ "type": "natural" }
],
- "sDom": "RZtir",
+ "buttons": [
+ 'csvHtml5'
+ ],
+ "sDom": "RZBtir",
"iDisplayLength": -1,
"autoWidth": true,
"bLengthChange": true,
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 4803b17c..5d658bc7 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -61,10 +61,13 @@
<div class="form-group">
<label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label>
<div class="col-xs-10 controls input-append">
- <div class="col-xs-8">
- <select name="dataset" id="dataset" class="form-control span5" style="width: 450px !important;"></select>
+ <div class="col-xs-10">
+ <select name="dataset" id="dataset" class="form-control span5" style="width: 340px !important;"></select>
<i class="icon-question-sign"></i>
</div>
+ <div class="col-xs-2">
+ <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 75px !important;">Info</button>
+ </div>
</div>
</div>
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 29f69dea..9f7dd41f 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -1,204 +1,151 @@
-<?XML VERSION="1.0" ENCODING="UTF-8">
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<HTML>
-<HEAD>
-<TITLE>Mapping</TITLE>
+{% extends "base.html" %}
+{% block title %}Mapping Results{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+{% endblock %}
+{% from "base_macro.html" import header %}
+{% block content %}
+ {{ header("Whole Genome Mapping Results",
+ '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
-<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
-<META NAME="keywords" CONTENT="genetics, bioinformatics, genome, phenome, gene expression, complex trait analysis, gene mapping, SNP, quantitative trait locus QTL, expression eQTL, WebQTL, Traitnet, Traitnetwork, personalized medicine">
-<META NAME="description" CONTENT ="GeneNetwork is a free scientific web resource used to study relationships between differences in genes, environmental factors, phenotypes, and disease risk." >
-<META NAME="author" CONTENT ="GeneNetwork developers" >
-<META NAME="geo.placename" CONTENT ="Memphis, TN" >
-<META NAME="geo.region" CONTENT="US-TN">
+ <div class="container">
+ <form method="post" target="_blank" action="/marker_regression" name="marker_regression" id="marker_regression_form">
+ <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
+ <input type="hidden" name="trait_id" value="{{ this_trait.name }}">
+ <input type="hidden" name="dataset" value="{{ dataset.name }}">
+ {% for sample in dataset.group.samplelist %}
+ <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
+ {% endfor %}
+ <input type="hidden" name="maf">
+ <input type="hidden" name="method" value="{{ mapping_method }}">
+ <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
+ <input type="hidden" name="manhattan_plot">
+ <input type="hidden" name="num_perm">
+ <input type="hidden" name="do_control" value="{{ doControl }}">
+ <input type="hidden" name="control_marker" value="{{ controlLocus }}">
+ <input type="hidden" name="mapmethod_rqtl_geno" value="{{ mapmethod_rqtl_geno }}">
+ <input type="hidden" name="mapmodel_rqtl_geno" value="{{ mapmodel_rqtl_geno }}">
+ <input type="hidden" name="pair_scan" value="{{ pair_scan }}">
+ <div id="chart_container">
+ <div class="qtlcharts" id="topchart">
+ {{ gifmap|safe }}
+ <img src="/static/output/{{ filename }}.jpeg" usemap="#WebQTLImageMap">
+ </div>
+ </div>
+ </form>
+ <div style="width:48%;">
+ <h2>
+ Results
+ </h2>
+ <table id="qtl_results" class="table table-hover table-striped">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Index</th>
+ <th>{{ LRS_LOD }}</th>
+ <th>Chr</th>
+ {% if plotScale == "centimorgan" %}
+ <th>cM</th>
+ {% else %}
+ <th>Mb</th>
+ {% endif %}
+ <th>Locus</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for marker in qtlresults %}
+ {% if (LRS_LOD == "LOD" and marker.lod_score|float > cutoff|float) or
+ (LRS_LOD == "LRS" and marker.lrs_value|float > cutoff|float) %}
+ <tr>
+ <td>
+ <input type="checkbox" name="selectCheck"
+ class="checkbox edit_sample_checkbox"
+ value="{{ marker.name }}" checked="checked">
+ </td>
+ <Td align="right">{{ loop.index }}</Td>
+ {% if LRS_LOD == "LOD" %}
+ <td>{{ '%0.2f' | format(marker.lod_score|float) }}</td>
+ {% else %}
+ <td>{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
+ {% endif %}
+ <td>{{marker.chr}}</td>
+ <td>{{ '%0.6f' | format(marker.Mb|float) }}</td>
+ <td>
+ {{ marker.name }}
+ <!--<a href="{{ url_for('show_trait_page',
+ trait_id = marker.name,
+ dataset = dataset.name
+ )}}">
+ {{ marker.name }}
+ </a>-->
+ </td>
+ </tr>
+ {% endif %}
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ </div>
-<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'>
-<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'>
-<link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" />
-<LINK REL="apple-touch-icon" href="/images/ipad_icon3.png" />
-<link type="text/css" href='/css/custom-theme/jquery-ui-1.10.3.custom.css' rel='Stylesheet' />
-<link type="text/css" href='/css/tab_style.css' rel='Stylesheet' />
+ <!-- End of body -->
-<script type="text/javascript" src="/javascript/jquery-1.5.2.min.js"></script>
-<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT>
-<SCRIPT SRC="/javascript/dhtml.js"></SCRIPT>
-<SCRIPT SRC="/javascript/tablesorter.js"></SCRIPT>
-<SCRIPT SRC="/javascript/jqueryFunction.js"></SCRIPT>
-<script src="/javascript/tabbed_pages.js" type="text/javascript"></script>
-<script src="/javascript/jquery-ui-1.10.3.custom.min.js" type="text/javascript"></script>
-<script src="/javascript/sorttable.js"></script>
+{% endblock %}
-</HEAD>
-<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff >
+{% block js %}
-<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0>
- <TBODY>
- <!-- Start of body -->
- <TR>
- <TD bgColor=#eeeeee class="solidBorder">
- <Table width= "100%" cellSpacing=0 cellPadding=5>
- <TR>
- <TD height="200" bgcolor="#eeeeee">
- <BLOCKQUOTE>
- <TABLE border="0" cellpadding="0" cellspacing="0">
- <TR>
- <TD valign="top">
- <P class="title">Map Viewer: Whole Genome</P>
- <P>
- <STRONG>Population: </STRONG>{{ dataset.species }} {{ dataset.group.name }}<BR>
- <STRONG>Database: </STRONG><A HREF="http://www.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName={{ dataset.name }}" TARGET="_blank" class="normalsize">{{ dataset.fullname }}</A><BR>
- <STRONG>Trait ID: </STRONG><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = dataset.name) }}">{{ marker.name }}</a><BR>
- {% if this_trait.symbol != None %}
- <STRONG>Gene Symbol: </STRONG><EM id="green">this_trait.symbol</EM><BR>
- {% if this_trait.dataset.type != 'Publish' %}
- <STRONG>Location: </STRONG> {{ this_trait.location_fmt }}
- {% endif %}
- </P>
- <P>
- <BR><A HREF="/tmp/Itvl_bnCx5c3U.txt" TARGET="_blank" class="smallsize">Download</A> results in tab-delimited text format.</TD><TD width="25">&nbsp;</TD><TD class="doubleBorder" width="400">
-<FORM METHOD="POST" ACTION="/webqtl/main.py" ENCTYPE="multipart/form-data" NAME="changeViewForm">
-<TABLE border="0"><TR><TD valign="top"><TABLE border="0"><TR><TD class="fs12 fwb ffl">Chr: </TD><TD><SELECT NAME="chromosomes" SIZE=1 onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);">
-<OPTION Value="-1" SELECTED>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>
-<SELECT NAME="scale" SIZE=1 onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);">
-<OPTION Value="morgan">Genetic</OPTION>
-<OPTION Value="physic" SELECTED>Physical</OPTION>
-</SELECT>
+ <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>
-<INPUT TYPE="button" NAME="Default_Name" class="button" VALUE="Remap" onClick="javascript:databaseFunc(this.form,'showIntMap');"></TD></TR><TR><TD class="fs12 fwb ffl">View: </TD><TD nowrap="on">
-<INPUT TYPE="text" NAME="startMb" SIZE=10> to
-<INPUT TYPE="text" NAME="endMb" SIZE=10>Mb<SPAN class="cr"> *</SPAN></TD></TR><TR><TD class="fs12 fwb ffl">Units: </TD><TD>
-<INPUT TYPE="radio" NAME="LRSCheck" VALUE="LRS" CHECKED>LRS
-<INPUT TYPE="radio" NAME="LRSCheck" VALUE="LOD">LOD <A HREF="/glossary.html#LOD" TARGET="helpWind"><IMG src="/images/qmarkBoxBlue.gif" height="13" width="10" alt="Glossary" border="0"></A></TD></TR><TR><TD class="fs12 fwb ffl"> </TD><TD class="fs11 fwn">
-<INPUT TYPE="text" NAME="lrsMax" VALUE="0.0" SIZE=3>units on Y-axis (0 for default)</TD></TR><TR><TD class="fs12 fwb ffl">Width: </TD><TD class="fs11 fwn ">
-<INPUT TYPE="text" NAME="graphWidth" VALUE="1600" SIZE=5>pixels (minimum=1400)</TD></TR></TABLE></TD><TD width="15">&nbsp;</TD><TD nowrap="on" valign="top">
-<INPUT TYPE="checkbox" NAME="permCheck" class="checkbox" VALUE="ON" CHECKED><SPAN class="fs12 fwn">Permutation Test <A HREF="/glossary.html#Permutation" TARGET="helpWind"><IMG src="/images/qmarkBoxBlue.gif" height="13" width="10" alt="Glossary" border="0"></A></SPAN><BR>
-<INPUT TYPE="checkbox" NAME="bootCheck" class="checkbox" VALUE="ON" CHECKED><SPAN class="fs12 fwn">Bootstrap Test <A HREF="/glossary.html#bootstrap" TARGET="helpWind"><IMG src="/images/qmarkBoxBlue.gif" height="13" width="10" alt="Glossary" border="0"></A></SPAN><BR>
-<INPUT TYPE="checkbox" NAME="additiveCheck" class="checkbox" VALUE="ON" CHECKED><SPAN class="fs12 fwn">Allele Effects <A HREF="/glossary.html#additive" TARGET="helpWind"><IMG src="/images/qmarkBoxBlue.gif" height="13" width="10" alt="Glossary" border="0"></A></SPAN><BR>
-<INPUT TYPE="checkbox" NAME="showSNP" class="checkbox" VALUE="ON" CHECKED><SPAN class="fs12 fwn">SNP Track <A HREF="/glossary.html#snpSeismograph" TARGET="helpWind"><IMG src="/images/qmarkBoxBlue.gif" height="13" width="10" alt="Glossary" border="0"></A></SPAN><SPAN class="cr"> *</SPAN><BR>
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-<P>
-<P id="smallsize"><BR>A positive additive coefficient (<FONT color="green">green</FONT> line) indicates that DBA/2J alleles increase trait values. In contrast, a negative additive coefficient (<FONT color="red">red</FONT> line) indicates that C57BL/6J alleles increase trait values.</P>
-<P>
-<TABLE><TR><TD><IMG src="/image/Reg_9sObQtW0.gif" alt="Histogram of Permutation Test" border="0"></TD></TR><TR><TD></TD></TR><TR><TD>Total of 1000 permutations</TD></TR></TABLE>
-<P>
-<A HREF="/tmp/Reg_1MWrEXK7.txt" TARGET="_blank" class="fs12 fwn">Download Permutation Results</A></BLOCKQUOTE></TD>
- </TR>
- </TABLE>
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+ <script>
+ js_data = {{ js_data | safe }}
+ </script>
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+ <script type="text/javascript" charset="utf-8">
+ $(document).ready( function () {
+ console.time("Creating table");
+ $('#qtl_results').dataTable( {
+ "columns": [
+ { "type": "natural", "sWidth": "10%", "bSortable": false },
+ { "type": "natural" },
+ { "type": "natural" },
+ { "type": "natural" },
+ { "type": "natural" },
+ { "type": "natural", "sWidth": "30%"}
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+ "buttons": [
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+ "iDisplayLength": -1,
+ "autoWidth": true,
+ "bDeferRender": true,
+ "bSortClasses": false,
+ "scrollY": "700px",
+ "scrollCollapse": true,
+ "paging": false
+ } );
+ console.timeEnd("Creating table");
+
+ });
+
+ chrView = function(this_chr, chr_mb_list) {
+ $('input[name=selected_chr]').val(this_chr + 1)
+ $('input[name=chr_mb_list]').val(chr_mb_list)
+
+ return $('#marker_regression_form').submit();
+ };
+
+ </script>
+
+{% endblock %}
-<!-- menu script itself. you should not modify this file -->
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-<!-- items structure. menu hierarchy and links are stored there -->
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diff --git a/wqflask/wqflask/templates/marker_regression_old.html b/wqflask/wqflask/templates/marker_regression_old.html
deleted file mode 100644
index defcd929..00000000
--- a/wqflask/wqflask/templates/marker_regression_old.html
+++ /dev/null
@@ -1,106 +0,0 @@
-{% extends "base.html" %}
-{% block title %}Marker Regression{% endblock %}
-{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/packages/jqplot/jquery.jqplot.min.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
- <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
- <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
-{% endblock %}
-{% block content %} <!-- Start of body -->
-
- {{ header("Marker Regression",
- '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
-
- <div class="container">
- <div>
- <h2>
- Manhattan Plot
- </h2>
- </div>
- <div id="manhattan_plot_container" class="manhattan_plot_container">
- <div id="manhattan_plot" class="manhattan_plots">
-
- </div>
- </div>
- <div>
- <h2>
- Genome Association Results
- </h2>
- </div>
-
- <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <td>Index</td>
- <td>LOD Score</td>
- <td>Chr</td>
- <td>Mb</td>
- <td>Locus</td>
- </tr>
- </thead>
- <tbody>
- {% for marker in filtered_markers %}
- {% if marker.lod_score > lod_cutoff %}
- <tr>
- <td>{{loop.index}}</td>
- <td>{{marker.lod_score}}</td>
- <td>{{marker.chr}}</td>
- <td>{{marker.Mb}}</td>
- <td>{{marker.name}}</td>
- </tr>
- {% endif %}
- {% endfor %}
- </tbody>
- </table>
- </div>
-
- <!-- End of body -->
-
-{% endblock %}
-
-{% block js %}
- <script>
- js_data = {{ js_data | safe }}
- </script>
-
- <!--[if lt IE 9]>
-<!-- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
- <![endif]-->
- <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_manhattan_plot.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/marker_regression.js"></script>
-
-
- <script type="text/javascript" charset="utf-8">
- $(document).ready( function () {
- console.time("Creating table");
- $('#qtl_results').dataTable( {
- //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
- "sDom": "lTftipr",
- "oTableTools": {
- "aButtons": [
- "copy",
- "print",
- {
- "sExtends": "collection",
- "sButtonText": 'Save <span class="caret" />',
- "aButtons": [ "csv", "xls", "pdf" ]
- }
- ],
- "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
- },
- "iDisplayLength": 50,
- "bLengthChange": true,
- "bDeferRender": true,
- "bSortClasses": false
- } );
- console.timeEnd("Creating table");
- });
- </script>
-{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index a66a85d6..e9dd4ab1 100755
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -61,7 +61,6 @@
</form>
</div>
- </div>
</div>
{% endblock %}
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
deleted file mode 100755
index fe6f3f65..00000000
--- a/wqflask/wqflask/templates/quick_search.html
+++ /dev/null
@@ -1,300 +0,0 @@
-{% extends "base.html" %}
-{% block title %}QuickSearch Results{% endblock %}
-{% block content %}
-<!-- Start of body -->
-
- {{ header("QuickSearch Results") }}
-
- <div class="container">
- <div class="page-header">
- <h1>Your Search</h1>
- </div>
-
- <p>We searched across all data sets to find all records that match:</p>
-
- <ul>
- {% if search_terms %}
- <li>
- <strong>{{search_terms}}</strong>
- </li>
- {% endif %}
- </ul>
-
-
- <div class="tabbable"> <!-- Only required for left/right tabs -->
- {% if trait_type == 'all' %}
- {% include 'all_results.html' %}
- {% else %}
- <ul class="nav nav-tabs">
- {% for species in species_groups %}
- <li> <a href="#tab{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
- {% endfor %}
- </ul>
- <div class="tab-content">
- {% for species in species_groups %}
- <div class="tab-pane active" id="tab{{ loop.index }}">
- <div>
- {#
- <ul class="nav nav-tabs">
- {% if species_groups[species]['phenotype'] %}
- <li class="active"> <a href="#tab{{ loop.index }}_1" data-toggle="tab">Phenotype</a></li>
- {% endif %}
- {% if species_groups[species]['mrna_assay'] %}
- <li> <a href="#tab{{ loop.index }}_2" data-toggle="tab">mRNA Assay</a></li>
- {% endif %}
- {% if species_groups[species]['genotype'] %}
- <li> <a href="#tab{{ loop.index }}_3" data-toggle="tab">Genotype</a></li>
- {% endif %}
- </ul>
- #}
- <div>
- {% if trait_type == 'phenotype' and species_groups[species]['phenotype'] %}
- <table id="pheno_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <th>Id</th>
- <th>Species</th>
- <th>Group</th>
- <th>Description</th>
- <th>LRS</th>
- <th>Year</th>
- <th>Authors</th>
- </tr>
- </thead>
- <tbody>
- {% for result in results.phenotype %}
- {% if result.result_fields['species'] == species %}
- <tr>
- <td>{{ result.result_fields['phenotype_id'] }}</td>
- <td>{{ result.result_fields['species'] }}</td>
- <td>{{ result.result_fields['group_name'] }}</td>
- <td>{{ result.result_fields['description'] }}</td>
- <td>{{ result.result_fields['lrs'] }}</td>
- <td>
- <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract">
- {{ result.result_fields['year'] }}
- </a>
- </td>
- <td>{{ result.result_fields['authors'] }}</td>
- </tr>
- {% endif %}
- {% endfor %}
- </tbody>
- </table>
- {% endif %}
- {% if trait_type == 'mrna_assay' and species_groups[species]['mrna_assay'] %}
- <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <th>Record ID</th>
- <th>Species</th>
- <th>Group</th>
- <th>Data Set</th>
- <th>Symbol</th>
- <th>Description</th>
- <th>Location</th>
- <th>Mean Expr</th>
- <th>Max LRS</th>
- </tr>
- </thead>
- <tbody>
- {% for result in results.mrna_assay %}
- {% if result.result_fields['species'] == species %}
- <tr>
- <td>
- <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
- {{ result.result_fields['name'] }}
- </a>
- </td>
- <td>{{ result.result_fields['species'] }}</td>
- <td>{{ result.result_fields['group_name'] }}</td>
- <td>{{ result.result_fields['dataset_name'] }}</td>
- <td>{{ result.result_fields['symbol'] }}</td>
- <td>{{ result.result_fields['description'] }}</td>
- <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
- <td>{{ result.result_fields['mean'] }}</td>
- <td>{{ result.result_fields['lrs'] }}</td>
- </tr>
- {% endif %}
- {% endfor %}
- </tbody>
- </table>
- {% endif %}
- {% if trait_type == 'genotype' and species_groups[species]['genotype'] %}
- <table id="geno_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <th>Marker</th>
- <th>Species</th>
- <th>Group</th>
- <th>Data Set</th>
- <th>Location</th>
- </tr>
- </thead>
- <tbody>
- {% for result in results.genotype %}
- {% if result.result_fields['species'] == species %}
- <tr>
- <td>
- <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}">
- {{ result.result_fields['marker_name'] }}
- </a>
- </td>
- <td>{{ result.result_fields['species'] }}</td>
- <td>{{ result.result_fields['group_name'] }}</td>
- <td>{{ result.result_fields['dataset_name'] }}</td>
- <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td>
- </tr>
- {% endif %}
- {% endfor %}
- </tbody>
- </table>
- {% endif %}
- </div>
- </div>
- </div>
- {% endfor %}
- </div>
- {% endif %}
- </div>
- </div>
-
-<!-- End of body -->
-
-{% endblock %}
-
- {#
- <table id="pheno_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <th>Id</th>
- <th>Species</th>
- <th>Group</th>
- <th>Description</th>
- <th>LRS</th>
- <th>Year</th>
- <th>Authors</th>
- </tr>
- </thead>
- <tbody>
- {% for result in results.phenotype %}
- <tr>
- <td>{{ result.result_fields['phenotype_id'] }}</td>
- <td>{{ result.result_fields['species'] }}</td>
- <td>{{ result.result_fields['group_name'] }}</td>
- <td>{{ result.result_fields['description'] }}</td>
- <td>{{ result.result_fields['lrs'] }}</td>
- <td>
- <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract">
- {{ result.result_fields['year'] }}
- </a>
- </td>
- <td>{{ result.result_fields['authors'] }}</td>
- </tr>
- {% endfor %}
- </tbody>
- </table>
- </div>
- <div class="tab-pane" id="tab2">
- <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <th>Record ID</th>
- <th>Species</th>
- <th>Group</th>
- <th>Data Set</th>
- <th>Symbol</th>
- <th>Description</th>
- <th>Location</th>
- <th>Mean Expr</th>
- <th>Max LRS</th>
- </tr>
- </thead>
- <tbody>
- {% for result in results.mrna_assay %}
- <tr>
- <td>
- <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
- {{ result.result_fields['name'] }}
- </a>
- </td>
- <td>{{ result.result_fields['species'] }}</td>
- <td>{{ result.result_fields['group_name'] }}</td>
- <td>{{ result.result_fields['dataset_name'] }}</td>
- <td>{{ result.result_fields['symbol'] }}</td>
- <td>{{ result.result_fields['description'] }}</td>
- <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
- <td>{{ result.result_fields['mean'] }}</td>
- <td>{{ result.result_fields['lrs'] }}</td>
- </tr>
- {% endfor %}
- </tbody>
- </table>
- </div>
- <div class="tab-pane" id="tab3">
- <table id="geno_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <th>Marker</th>
- <th>Species</th>
- <th>Group</th>
- <th>Data Set</th>
- <th>Location</th>
- </tr>
- </thead>
- <tbody>
- {% for result in results.genotype %}
- <tr>
- <td>
- <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}">
- {{ result.result_fields['marker_name'] }}
- </a>
- </td>
- <td>{{ result.result_fields['species'] }}</td>
- <td>{{ result.result_fields['group_name'] }}</td>
- <td>{{ result.result_fields['dataset_name'] }}</td>
- <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td>
- </tr>
- {% endfor %}
- </tbody>
- </table>
- </div>
- #}
-
-
-{% block js %}
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
-
- <script type="text/javascript" charset="utf-8">
- $(document).ready( function () {
- console.time("Creating table");
- $('#pheno_results, #mrna_assay_results, #geno_results').dataTable( {
- //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
- //"sDom": "lTftipr",
- "oTableTools": {
- "aButtons": [
- "copy",
- "print",
- {
- "sExtends": "collection",
- "sButtonText": 'Save <span class="caret" />',
- "aButtons": [ "csv", "xls", "pdf" ]
- }
- ],
- "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
- },
- "iDisplayLength": 50,
- "bLengthChange": true,
- "bDeferRender": true,
- "bSortClasses": false
- } );
- console.timeEnd("Creating table");
- });
- </script>
-{% endblock %}
-
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 7b3df00f..02365b1d 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -16,10 +16,33 @@
<input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
<!-- Need to customize text more for other types of searches -->
- <p>We searched <a href="/static/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a>
- to find all records that match
+ <p>We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId={{dataset.id}}">{{ dataset.fullname }}</a>
+ to find all records
{% for word in search_terms %}
- <strong>{{word.search_term[0]}}</strong> {% if not loop.last %} or {% endif %}
+ {% if word.key|lower == "rif" %}
+ with <u>GeneRIF</u> containing <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.key|lower == "go" %}
+ with <u>Gene Ontology ID</u> <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.key|lower == "wiki" %}
+ with <u>GeneWiki</u> containing <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.key|lower == "mean" %}
+ with <u>MEAN</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.key|lower == "lrs" or word.key|lower == "translrs" or word.key|lower == "cislrs" %}
+ {% if word.search_term|length == 1 %}
+ with {% if word.key|lower == "translrs" %}trans{% elif word.key|lower == "cislrs" %}cis{% endif %}LRS {% if word.separator == ">" %} greater than {% elif word.separator == "<" %} less than {% elif word.separator == ">=" %} greater than or equal to {% elif word.separator == "<=" %} less than or equal to {% endif %} <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.search_term|length == 2 %}
+ with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.search_term|length == 3 %}
+ with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.search_term|length == 5 %}
+ with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong> between <strong>{{ word.search_term[3] }}</strong> and <strong>{{ word.search_term[4] }}</strong> Mb{% if not loop.last %} and {% endif %}
+ {% endif %}
+ {% elif word.key|lower == "position" %}
+ with <u>target genes</u> on chromosome <strong>{% if word.search_term[0].split('chr')|length > 1 %}{{ word.search_term[0].split('chr')[1] }}{% elif word.search_term[0].split('CHR')|length > 1 %}{{ word.search_term[0].split('CHR')[1] }}{% else %}{{ word.search_term[0] }}{% endif %}</strong> between <strong>{{ word.search_term[1] }}</strong> and <strong>{{ word.search_term[2] }}</strong> Mb{% if not loop.last %} and {% endif %}
+ {% else %}
+ with {{ word.key|lower }} matching {{ word.search_term[0] }}
+ {% endif %}
+ <!--<strong>{{word.search_term[0]}}</strong> {% if not loop.last %} or {% endif %}-->
{% endfor %}.
</p>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index a86a149d..29239adb 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -1,12 +1,10 @@
{% extends "base.html" %}
{% block title %}Trait Data and Analysis{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/bar_chart.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/nvd3/nv.d3.min.css" />
@@ -27,7 +25,7 @@
{% endif %}
- <form method="post" action="/corr_compute" name="trait_page" id="trait_data_form"
+ <form method="post" target="_blank" action="/corr_compute" name="trait_page" id="trait_data_form"
class="form-horizontal">
<div id="hidden_inputs">
<input type="hidden" name="trait_hmac" value="{{ data_hmac('{}:{}'.format(this_trait.name, dataset.name)) }}">
@@ -50,7 +48,7 @@
</div>
<div id="collapseOne" class="panel-collapse collapse in">
<div class="panel-body">
- {% include 'show_trait_statistics_new.html' %}
+ {% include 'show_trait_statistics.html' %}
</div>
</div>
</div>
@@ -115,8 +113,6 @@
<script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script>
<script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
<script type="text/javascript" src="/static/new/javascript/colorbrewer.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/panelutil.js"></script>
<script type="text/javascript" src="/static/new/javascript/stats.js"></script>
<script type="text/javascript" src="/static/new/javascript/box.js"></script>
@@ -136,9 +132,6 @@
<script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
<script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
@@ -196,8 +189,6 @@
}
});
- console.time("Creating table");
-
$('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'yellow')
{% if sample_groups[0].se_exists() %}
$('#samples_primary, #samples_other').DataTable( {
@@ -225,10 +216,8 @@
},
"paging": false
} );
- console.timeEnd("Creating table");
{% else %}
- console.time("Creating table");
$('#samples_primary, #samples_other').DataTable( {
"columns": [
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 68cc8b18..a7edbc48 100755
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -72,7 +72,6 @@
</select>
</div>
</div>
- {% if this_trait.dataset.type == 'ProbeSet' %}
<div class="form-group">
<label class="col-xs-1 control-label">Min Expr</label>
<div class="col-xs-2 controls">
@@ -89,7 +88,6 @@
<br>
</div>
</div>
- {% endif %}
<div class="form-group">
<label class="col-xs-1 control-label">Range</label>
<div class="col-xs-3 controls">
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index de25f4ee..c23cb010 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -187,6 +187,24 @@
<input name="num_perm_reaper" value="2000" type="text" class="form-control">
</div>
</div>
+ <div class="mapping_method_fields form-group">
+ <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+ {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
+ <input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
+ {% else %}
+ <input name="control_reaper" value="" type="text" class="form-control" />
+ {% endif %}
+ <label class="radio-inline">
+ <input type="radio" name="do_control_reaper" value="true">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="do_control_reaper" value="false" checked="">
+ No
+ </label>
+ </div>
+ </div>
<!--
<div class="mapping_method_fields form-group">
<label for="mapping_bootstraps" class="col-xs-3 control-label" title="Bootstrapping Resamples">Bootstrap</label>
@@ -225,7 +243,7 @@
</div>
<div class="form-group">
<div style="padding-left:15px;" class="controls">
- <button id="interval_mapping_compute" class="btn submit_special btn-primary" data-url="/interval_mapping" title="Compute Interval Mapping">
+ <button id="interval_mapping_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Interval Mapping">
<i class="icon-ok-circle icon-white"></i> Compute
</button>
</div>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index eda5466e..2183dd30 100755
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -1,433 +1,155 @@
-<br />
-
<div>
- <h2>Basic Statistics</h2>
-
+ <div class="tabbable"> <!-- Only required for left/right tabs -->
+ <ul class="nav nav-pills">
+ <li class="active">
+ <a href="#stats_tab" data-toggle="tab">Basic Statistics</a>
+ </li>
+ <li>
+ <a href="#histogram_tab" data-toggle="tab">Histogram</a>
+ </li>
+ <li>
+ <a href="#bar_chart_tab" data-toggle="tab">Bar Chart</a>
+ </li>
+ <li>
+ <a href="#probability_plot" data-toggle="tab">Probability Plot</a>
+ </li>
+ {% if g.user_session.user_ob %}
+ <li>
+ <a href="#scatterplot_matrix" data-toggle="tab">Scatterplot Matrix</a>
+ </li>
+ {% endif %}
+ <!--<li>
+ <a href="#box_plot_tab" data-toggle="tab">Box Plot</a>
+ </li>-->
+ </ul>
- <p id="sectionbody2"></p>Include:
- <select name="corr_samples_group" size="1">
+ <div class="tab-content">
+ <div class="tab-pane active" id="stats_tab">
+ <div style="padding: 20px" class="form-horizontal">
+ <table id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped"></table>
+
+ </div>
+ </div>
+ <div class="tab-pane" id="histogram_tab">
+ <div style="padding: 20px" class="form-horizontal">
+ {% if sample_groups|length != 1 %}
+ <select class="histogram_samples_group">
{% for group, pretty_group in sample_group_types.items() %}
- <option value="{{ group }}">
- {{ pretty_group }}
- </option>
+ <option value="{{ group }}">{{ pretty_group }}</option>
{% endfor %}
- </select><br>
- <br>
- <input type="button" name="Default_Name" class="btn update" value=" Update Figures "><br>
- <br>
-
- {% 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>
-
- <li><a href="#statstabs-5" class="stats_tab">Probability Plot</a></li>
-
- <li><a href="#statstabs-3" class="stats_tab">Bar Graph (by name)</a></li>
-
- <li><a href="#statstabs-4" class="stats_tab">Bar Graph (by rank)</a></li>
-
- <li><a href="#statstabs-2" class="stats_tab">Box Plot</a></li>
- </ul>
-
- <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="fs14 fwb ffl b1 cw cbrb" align="right" width="60">Value</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" align="left">N of Samples</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>
-
- <li><a href="#statstabs-5" class="stats_tab">Probability Plot</a></li>
-
- <li><a href="#statstabs-3" class="stats_tab">Bar Graph (by name)</a></li>
-
- <li><a href="#statstabs-4" class="stats_tab">Bar Graph (by rank)</a></li>
-
- <li><a href="#statstabs-2" class="stats_tab">Box Plot</a></li>
- </ul>
-
- <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="fs14 fwb ffl b1 cw cbrb" align="right" width="60">Value</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" align="left">N of Samples</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>
-
- <div class="ui-tabs" id="stats_tabs2">
-
-
- <ul>
- <li><a href="#statstabs-1" class="stats_tab">Basic Table</a></li>
-
- <li><a href="#statstabs-5" class="stats_tab">Probability Plot</a></li>
-
- <li><a href="#statstabs-3" class="stats_tab">Bar Graph (by name)</a></li>
-
- <li><a href="#statstabs-4" class="stats_tab">Bar Graph (by rank)</a></li>
-
- <li><a href="#statstabs-2" class="stats_tab">Box Plot</a></li>
- </ul>
-
- <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="fs14 fwb ffl b1 cw cbrb" align="right" width="60">Value</td>
- </tr>
-
- <tr align="right">
- <td class="fs13 b1 cbw c222" align="left">N of Samples</td>
-
- <td class="fs13 b1 cbw c222" nowrap="yes">32</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">6.176</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">6.170</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">0.027</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">0.150</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">5.906</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">6.485</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">0.579</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>
+ </select>
+ <br><br>
+ {% endif %}
+ <div id="histogram_container">
+ <div id="histogram" class="barchart"></div>
+ </div>
+ </div>
+ </div>
+ <div class="tab-pane" id="bar_chart_tab">
+ <div style="padding: 20px" class="form-horizontal">
+ {% if sample_groups|length != 1 %}
+ <select class="bar_chart_samples_group">
+ {% for group, pretty_group in sample_group_types.items() %}
+ <option value="{{ group }}">{{ pretty_group }}</option>
+ {% endfor %}
+ </select>
+ {% endif %}
+ {% if sample_groups[0].attributes %}
+ <div class="input-append">
+ <select id="color_attribute" size="1">
+ <option value="None">None</option>
+ {% 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>
+ </div>
+ {% endif %}
+ <div id="update_bar_chart" class="btn-group">
+ <button type="button" class="btn btn-default sort_by_name" value="name">
+ <i class="icon-resize-horizontal"></i> Sort By Name
+ </button>
+ <button type="button" class="btn btn-default sort_by_value" value="value">
+ <i class="icon-signal"></i> Sort By Value
+ </button>
+ </div>
+ {% if g.user_session.user_ob %}
+ <div class="btn-group">
+ <button type="button" class="btn btn-default" id="color_by_trait">
+ <i class="icon-tint"></i> Color by Trait
+ </button>
+ </div>
+ {% endif %}
+ </div>
+ <div class="row" style="position:relative">
+ <div id="bar_chart_legend" style="margin-left: 150px; margin-top:20px; position: absolute;">
+ <span id="legend-left"></span>
+ <span id="legend-colors"></span>
+ <span id="legend-right"></span>
+ </div>
+ </div>
+ <div style="margin-left: 20px; margin-right: 20px;" class="row" id="bar_chart_container">
+ <svg></svg>
+ </div>
+ </div>
+ <div class="tab-pane" id="probability_plot">
+ <div style="padding: 20px" class="form-horizontal">
+ {% if sample_groups|length != 1 %}
+ <select class="prob_plot_samples_group">
+ {% for group, pretty_group in sample_group_types.items() %}
+ <option value="{{ group }}">{{ pretty_group }}</option>
+ {% endfor %}
+ </select>
+ <br><br>
+ {% endif %}
+
+ <div id="prob_plot_container">
+ <div id="prob_plot_title"></div>
+ <svg></svg>
+ </div>
+
+ <div>
+ 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>
+ </div>
+
+ </div>
+
+ </div>
+<!-- <div class="tab-pane" id="box_plot_tab">
+ {% if sample_groups|length > 1 %}
+ <select class="box_plot_samples_group">
+ {% for group, pretty_group in sample_group_types.items() %}
+ <option value="{{ group }}">{{ pretty_group }}</option>
+ {% endfor %}
+ </select>
+ <br><br>
+ {% endif %}
+ <div id="box_plot_container">
+ <div id="box_plot"></div>
+ </div>
+ </div>-->
+ {% if g.user_session.user_ob %}
+ <div class="tab-pane" id="scatterplot_matrix">
+
+ <div style="margin-bottom:40px;" class="btn-group">
+ <button type="button" class="btn btn-default" id="select_compare_trait">
+ <i class="icon-th-large"></i> Select Traits
+ </button>
+ <button type="button" class="btn btn-default" id="clear_compare_trait">
+ <i class="icon-trash"></i> Clear
+ </button>
+ </div>
+ <div id="scatterplot_container">
+ <div id="comparison_scatterplot" class="qtlcharts"></div>
+ </div>
+ </div>
+ {% endif %}
</div>
- </div>
- </td>
- </tr>
- </table>
- #}
+ </div>
+ <!--</div>-->
+ <div id="collections_holder_wrapper" style="display:none;">
+ <div id="collections_holder"></div>
+ </div>
+
+</div>
diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html
deleted file mode 100755
index 34fa2216..00000000
--- a/wqflask/wqflask/templates/show_trait_statistics_new.html
+++ /dev/null
@@ -1,155 +0,0 @@
-<div>
- <div class="tabbable"> <!-- Only required for left/right tabs -->
- <ul class="nav nav-pills">
- <li class="active">
- <a href="#stats_tab" data-toggle="tab">Basic Statistics</a>
- </li>
- <li>
- <a href="#histogram_tab" data-toggle="tab">Histogram</a>
- </li>
- <li>
- <a href="#bar_chart_tab" data-toggle="tab">Bar Chart</a>
- </li>
- <li>
- <a href="#probability_plot" data-toggle="tab">Probability Plot</a>
- </li>
- {% if g.user_session.user_ob %}
- <li>
- <a href="#scatterplot_matrix" data-toggle="tab">Scatterplot Matrix</a>
- </li>
- {% endif %}
- <!--<li>
- <a href="#box_plot_tab" data-toggle="tab">Box Plot</a>
- </li>-->
- </ul>
-
- <div class="tab-content">
- <div class="tab-pane active" id="stats_tab">
- <div style="padding: 20px" class="form-horizontal">
- <table id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped"></table>
-
- </div>
- </div>
- <div class="tab-pane" id="histogram_tab">
- <div style="padding: 20px" class="form-horizontal">
- {% if sample_groups|length != 1 %}
- <select class="histogram_samples_group">
- {% for group, pretty_group in sample_group_types.items() %}
- <option value="{{ group }}">{{ pretty_group }}</option>
- {% endfor %}
- </select>
- <br><br>
- {% endif %}
- <div id="histogram_container">
- <div id="histogram" class="barchart"></div>
- </div>
- </div>
- </div>
- <div class="tab-pane" id="bar_chart_tab">
- <div style="padding: 20px" class="form-horizontal">
- {% if sample_groups|length != 1 %}
- <select class="bar_chart_samples_group">
- {% for group, pretty_group in sample_group_types.items() %}
- <option value="{{ group }}">{{ pretty_group }}</option>
- {% endfor %}
- </select>
- {% endif %}
- {% if sample_groups[0].attributes %}
- <div class="input-append">
- <select id="color_attribute" size="1">
- <option value="None">None</option>
- {% 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>
- </div>
- {% endif %}
- <div id="update_bar_chart" class="btn-group">
- <button type="button" class="btn btn-default sort_by_name" value="name">
- <i class="icon-resize-horizontal"></i> Sort By Name
- </button>
- <button type="button" class="btn btn-default sort_by_value" value="value">
- <i class="icon-signal"></i> Sort By Value
- </button>
- </div>
- {% if g.user_session.user_ob %}
- <div class="btn-group">
- <button type="button" class="btn btn-default" id="color_by_trait">
- <i class="icon-tint"></i> Color by Trait
- </button>
- </div>
- {% endif %}
- </div>
- <div class="row" style="position:relative">
- <div id="bar_chart_legend" style="margin-left: 150px; margin-top:20px; position: absolute;">
- <span id="legend-left"></span>
- <span id="legend-colors"></span>
- <span id="legend-right"></span>
- </div>
- </div>
- <div style="margin-left: 20px; margin-right: 20px;" class="row" id="bar_chart_container">
- <svg></svg>
- </div>
- </div>
- <div class="tab-pane" id="probability_plot">
- <div style="padding: 20px" class="form-horizontal">
- {% if sample_groups|length != 1 %}
- <select class="prob_plot_samples_group">
- {% for group, pretty_group in sample_group_types.items() %}
- <option value="{{ group }}">{{ pretty_group }}</option>
- {% endfor %}
- </select>
- <br><br>
- {% endif %}
-
- <div id="prob_plot_container">
- <div id="prob_plot_title"></div>
- <svg></svg>
- </div>
-
- <div>
- 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>
- </div>
-
- </div>
-
- </div>
-<!-- <div class="tab-pane" id="box_plot_tab">
- {% if sample_groups|length > 1 %}
- <select class="box_plot_samples_group">
- {% for group, pretty_group in sample_group_types.items() %}
- <option value="{{ group }}">{{ pretty_group }}</option>
- {% endfor %}
- </select>
- <br><br>
- {% endif %}
- <div id="box_plot_container">
- <div id="box_plot"></div>
- </div>
- </div>-->
- {% if g.user_session.user_ob %}
- <div class="tab-pane" id="scatterplot_matrix">
-
- <div style="margin-bottom:40px;" class="btn-group">
- <button type="button" class="btn btn-default" id="select_compare_trait">
- <i class="icon-th-large"></i> Select Traits
- </button>
- <button type="button" class="btn btn-default" id="clear_compare_trait">
- <i class="icon-trash"></i> Clear
- </button>
- </div>
- <div id="scatterplot_container">
- <div id="comparison_scatterplot" class="qtlcharts"></div>
- </div>
- </div>
- {% endif %}
- </div>
- </div>
- <!--</div>-->
- <div id="collections_holder_wrapper" style="display:none;">
- <div id="collections_holder"></div>
- </div>
-
-</div>
diff --git a/wqflask/wqflask/templates/whats_new.html b/wqflask/wqflask/templates/whats_new.html
deleted file mode 100755
index 753c0d7d..00000000
--- a/wqflask/wqflask/templates/whats_new.html
+++ /dev/null
@@ -1,18 +0,0 @@
-{% extends "base.html" %}
-{% block title %}GeneNetwork{% endblock %}
-{% block content %}
-<!-- Start of body -->
-
- <!-- Body Start from Here -->
- <P class="title">Latest Updates and News from Genenetwork </P>
- {% for news_item in news_items %}
- <h4>{{ news_item.title }} ({{ news_item.date }})</h4>
- {{ news_item.details | safe }}
- <br /><br />
- {% endfor %}
-
-
-
-
-<!-- End of body -->
-{% endblock %}
generated by cgit v1.2.3 (git 2.47.1) at 2025-02-28 16:19:49 +0000