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-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html292
1 files changed, 125 insertions, 167 deletions
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 83454c08..9fa9257f 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -1,183 +1,141 @@
<div>
<h2>Mapping Tools</h2>
+ <div class="well form-horizontal">
+ <div class="tabbable"> <!-- Only required for left/right tabs -->
+ <ul class="nav nav-pills">
+ <li class="active">
+ <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
+ </li>
+ <li>
+ <a href="#marker_regression" data-toggle="tab">Marker Regression</a>
+ </li>
+ <li>
+ <a href="#pair_scan" data-toggle="tab">Pair Scan</a>
+ </li>
+ </ul>
+
+ <div class="tab-content">
+ <div class="tab-pane active" id="interval_mapping">
+ <div class="control-group">
+ <label for="chromosome" class="control-label">Chromosome:</label>
+ <div class="controls">
+ <select name="chromosome">
+ {% for name, value in dataset.species.chromosomes %}
+ <option value="{{ value }}">{{ name }}</option>
+ {% endfor %}
+ </select>
+ </div>
+ </div>
- <div class="tabbable"> <!-- Only required for left/right tabs -->
- <ul class="nav nav-tabs">
- <li class="active">
- <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
- </li>
- <li>
- <a href="#marker_regression" data-toggle="tab">Marker Regression</a>
- </li>
- <li>
- <a href="#pair_scan" data-toggle="tab">Pair Scan</a>
- </li>
- </ul>
-
- <div class="tab-content" style="padding-bottom: 9px; border-bottom: 1px solid #ddd;">
- <div class="tab-pane active" id="interval_mapping">
- <label for="chromosome">Chromosome: </label>
- <select name="chromosome">
- {% for name, value in dataset.species.chromosomes %}
- <option value="{{ value }}">{{ name }}</option>
- {% endfor %}
- </select>
- <br>
- {% if dataset.group.genotype.Mbmap %}
- <label for="scale">Scale: </label>
- <select name="scale">
- <option value="megabase">Megabase</option>
- <option value="centimorgan">Centimorgan</option>
- </select>
- {% endif %}
- <br>
-
- <label for="mapping_permutations">Permutation Test n=
- <input name="num_permutations" value="2000" />
- </label>
- <label for="mapping_bootstraps">Bootstrap Test n=
- <input name="mapping_bootstraps" value="2000" />
- </label>
-
- <br>
+ <div class="control-group">
+ <label for="mapping_permutations" class="control-label">Permutation Test n=</label>
+ <div class="controls">
+ <input name="num_permutations" value="2000" />
+ </div>
+ </div>
+
+ <div class="control-group">
+ <label for="mapping_bootstraps" class="control-label">Bootstrap Test n=</label>
+ <div class="controls">
+ <input name="mapping_bootstraps" value="2000" />
+ </div>
+ </div>
- <div class="well well-small">
- <strong>Composite Mapping</strong>
- - Control for a marker as a co-factor (e.g.: rs12345):
- <!--Prefer a <strong>composite</strong>? Tell us the control locus (e.g.: rs12345):-->
- <INPUT TYPE="text" NAME="control_locus" default="" />
+
+ {% if dataset.group.genotype.Mbmap %}
+ <div class="control-group">
+ <label class="control-label">Scale: </label>
+ <div class="controls">
+ <label class="radio inline">
+ <input type="radio" name="scale" id="scale" value="megabase" checked>
+ Megabase
+ </label>
+ <label class="radio inline">
+ <input type="radio" name="scale" id="scale" value="centimorgan">
+ Centimorgan
+ </label>
+ </div>
+ </div>
+ {% endif %}
+
+ <div class="well well-small">
+ <strong>Composite Mapping</strong>
+ - Control for a marker as a co-factor (e.g.: rs12345):
+ <!--Prefer a <strong>composite</strong>? Tell us the control locus (e.g.: rs12345):-->
+ <INPUT TYPE="text" NAME="control_locus" default="" />
+ </div>
+ <input type="button" name="interval_mapping_btn" class="btn" value="Compute">
+ </div>
+
+ <div class="tab-pane" id="marker_regression">
+ <label for="suggestive_lrs">Display LRS greater than:
+ <input name="suggestive_lrs" />
+ </label>
+ <label class="checkbox">
+ <input type="checkbox" name="display_all_lrs" /> Display All LRS
+ </label>
+ <input type="button" id="marker_regression_btn" name="marker_regression_btn" class="btn" value="Compute">
</div>
- <input type="button" name="interval_mapping_btn" class="btn" value="Compute">
- </div>
-
- <div class="tab-pane" id="marker_regression">
- <label for="suggestive_lrs">Display LRS greater than:
- <input name="suggestive_lrs" />
- </label>
- <label class="checkbox">
- <input type="checkbox" name="display_all_lrs" /> Display All LRS
- </label>
- <input type="button" id="marker_regression_btn" name="marker_regression_btn" class="btn" value="Compute">
-
-<!-- <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>
--->
- </div>
-
- <div class="tab-pane" id="pair_scan">
- <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>
+ <div class="tab-pane" id="pair_scan">
+ <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>
- <option value="1">
- LRS Interact
- </option>
- </select></td>
- </tr>
+ <td><select name="graphSort" size="1">
+ <option value="0">
+ LRS Full
+ </option>
- <tr>
- <td><span class="ffl fwb fs12"><strong>Return:</strong></span></td>
+ <option value="1">
+ LRS Interact
+ </option>
+ </select></td>
+ </tr>
- <td><select name="pairScanReturn" size="1">
- <option value="50">
- top 50
- </option>
+ <tr>
+ <td><span class="ffl fwb fs12"><strong>Return:</strong></span></td>
- <option value="100">
- top 100
- </option>
+ <td><select name="pairScanReturn" size="1">
+ <option value="50">
+ top 50
+ </option>
- <option value="200">
- top 200
- </option>
+ <option value="100">
+ top 100
+ </option>
- <option value="500">
- top 500
- </option>
- </select></td>
- </tr>
- </table><br>
- <label for="pairscan_permutations">Permutation Test n=
- <input name="pairscan_permutations" value="2000" />
- </label>
- <br>
- <br>
- <input type="button" class="btn" value=" Compute " onclick="dataEditingFunc(this.form,'directPlot');"><br>
- <br>
- </td>
- </tr>
+ <option value="200">
+ top 200
+ </option>
- <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>
+ <option value="500">
+ top 500
+ </option>
+ </select></td>
+ </tr>
+ </table><br>
+ <label for="pairscan_permutations">Permutation Test n=
+ <input name="pairscan_permutations" value="2000" />
+ </label>
+ <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>
</div>
</div>
</div>
-
-<!-- <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>
-
-
-
- <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>
-
-
- <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>-->