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| -rw-r--r-- | wqflask/wqflask/templates/show_trait_mapping_tools.html | 292 |
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>--> |