Merge branch 'feature/add_rqtl_pairscan' of github.com:zsloan/genenetwork2 into feature/add_rqtl_pairscan

2 files changed, 106 insertions, 1 deletions

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 059b0f31..7a6636c5 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -237,7 +237,8 @@ class RunMapping:
                 self.method = start_vars['mapmethod_rqtl']
             else:
                 self.method = "em"
-            self.model = start_vars['mapmodel_rqtl']
+            self.model = start_vars['mapmodel_rqtl_geno']
+            self.pair_scan = False
             if 'pair_scan' in start_vars:
                self.pair_scan = True
             if self.permCheck and self.num_perm > 0:
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 56c23a8b..80bc6509 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -456,6 +456,110 @@
                         </div>
                     </div>
                 </div>
+                <div class="tab-pane {% if dataset.group.mapping_id == '3' %}active{% endif %}" id="rqtl_pair">
+                    <div class="form-horizontal section-form-div">
+                        {% if genofiles and genofiles|length > 0 %}
+                        <div class="mapping_method_fields form-group">
+                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+                            <div class="col-xs-6 controls">
+                                <select id="genofile_rqtl_geno" class="form-control">
+                                    {% for item in genofiles %}
+                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
+                        {% endif %}
+                        <div class="mapping_method_fields form-group">
+                            <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
+                            <div class="col-xs-4 controls">
+                                <input name="num_perm_rqtl_geno" value="200" type="text" class="form-control">
+                            </div>
+                        </div>
+                        {% if sample_groups[0].attributes|length > 0 %}
+                        <div class="mapping_method_fields form-group">
+                            <label class="col-xs-3 control-label">Stratified</label>
+                            <div class="col-xs-6 controls">
+                                <label class="radio-inline">
+                                    <input type="radio" name="perm_strata" value="True" checked=""> 
+                                    Yes
+                                </label>
+                                <label class="radio-inline">
+                                    <input type="radio" name="perm_strata" value="False" >
+                                    No
+                               </label>
+                            </div>
+                        </div>
+                        {% endif %}
+                        <div class="mapping_method_fields form-group">
+                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
+                            <div class="col-xs-6 controls">
+                              <input name="control_rqtl_geno" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" />
+                              <label class="radio-inline">
+                                  <input type="radio" name="do_control_rqtl" value="true">
+                                  Yes
+                              </label>
+                              <label class="radio-inline">
+                                  <input type="radio" name="do_control_rqtl" value="false" checked="">
+                                  No
+                              </label>
+                            </div>
+                        </div>
+                        <div class="mapping_method_fields form-group">
+                            <label for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
+                            <div class="col-xs-4 controls">
+                              <select id="mapmodel_rqtl_geno" name="mapmodel_rqtl_geno" class="form-control">
+                                <option value="normal">Normal</option>
+                                {% if binary == "true" %}<option value="binary">Binary</option>{% endif %}
+                                <!--<option value="2part">2-part</option>-->
+                                <option value="np">Non-parametric</option>
+                              </select>
+                            </div>
+                        </div>
+                        <div class="mapping_method_fields form-group">
+                            <label for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label>
+                            <div class="col-xs-6 controls">
+                              <select id="mapmethod_rqtl_geno" name="mapmethod_rqtl_geno" class="form-control">
+                                <option value="hk" selected>Haley-Knott</option>
+                                <option value="ehk">Extended Haley-Knott</option>
+                                <option value="mr">Marker Regression</option>
+                                <option value="em">Expectation-Maximization</option>
+                                <option value="imp">Imputation</option>
+                              </select>
+                            </div>
+                        </div>
+                        <div id="missing_geno_div" class="mapping_method_fields form-group" style="display: none;">
+                            <label for="missing_genotypes" class="col-xs-3 control-label"></label>
+                            <div class="col-xs-6 controls">
+                              <select id="missing_genotype" name="missing_genotypes" class="form-control">
+                                <option value="mr">Remove Samples w/o Genotypes</option>
+                                <option value="mr-imp">Single Imputation</option>
+                                <option value="mr-argmax">Imputation w/ Viterbi Algorithm</option>
+                              </select>
+                            </div>
+                        </div>
+                        <div class="mapping_method_fields form-group">
+                          <label class="col-xs-3 control-label">Covariates<br><span class="covar-text">Select covariate(s) from a collection</span></label>
+                          <div class="col-xs-8 covar-options">
+                            {% if g.user_session.num_collections < 1 %}
+                            No collections available. Please add traits to a collection to use them as covariates.
+                            {% else %}
+                            <div class="select-covar-div">
+                              <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
+                              <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
+                            </div>
+                            <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
+                            {% endif %}
+                          </div>
+                        </div>
+                        <div class="mapping_method_fields form-group">
+                            <label class="col-xs-3 control-label"></label>
+                            <div class="col-xs-6 controls">
+                              <button id="rqtl_pair_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Pair Scan" value="Compute">Compute</button>
+                            </div>
+                        </div>
+                    </div>
+                </div>
                 {% endif %}
                 {% endfor %}
             </div>