diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 3 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_mapping_tools.html | 104 |
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 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> |