diff options
| -rwxr-xr-x | wqflask/wqflask/interval_mapping/interval_mapping.py | 9 | ||||
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 6 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_mapping_tools.html | 7 |
3 files changed, 13 insertions, 9 deletions
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py index 108bc747..46aac86c 100755 --- a/wqflask/wqflask/interval_mapping/interval_mapping.py +++ b/wqflask/wqflask/interval_mapping/interval_mapping.py @@ -92,10 +92,11 @@ class IntervalMapping(object): self.manhattan_plot = True else: self.manhattan_plot = False - if start_vars['display_additive'] == "yes": - self.additive = True - else: - self.additive = False + #ZS: Commenting this out until we can fix the issue with positive/negative additive effects being colored properly + #if start_vars['display_additive'] == "yes": + # self.additive = True + #else: + self.additive = False if 'control_locus' in start_vars: self.control_locus = start_vars['control_locus'] else: diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 1c5757a6..757aeb72 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -73,9 +73,11 @@ class MarkerRegression(object): self.suggestive = "" self.significant = "" self.pair_scan = False # Initializing this since it is checked in views to determine which template to use + self.score_type = "LRS" #ZS: LRS or LOD self.dataset.group.get_markers() if self.mapping_method == "gemma": + self.score_type = "LOD" included_markers, p_values = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals) self.dataset.group.get_specified_markers(markers = included_markers) self.dataset.group.markers.add_pvalues(p_values) @@ -83,6 +85,7 @@ class MarkerRegression(object): elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() elif self.mapping_method == "rqtl_geno": + self.score_type = "LOD" if start_vars['num_perm'] == "": self.num_perm = 0 else: @@ -136,7 +139,6 @@ class MarkerRegression(object): ) else: - self.score_type = "LRS" self.cutoff = 2 self.qtl_results = [] highest_chr = 1 #This is needed in order to convert the highest chr to X/Y @@ -165,7 +167,7 @@ class MarkerRegression(object): else: self.json_data['chr'].append(str(qtl['chr'])) self.json_data['pos'].append(qtl['Mb']) - if self.score_type == "LRS": + if 'lrs_value' in qtl: self.json_data['lod.hk'].append(str(qtl['lrs_value'])) else: self.json_data['lod.hk'].append(str(qtl['lod_score'])) diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index b9ac80bf..7f26a252 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -9,7 +9,7 @@ <a href="#pylmm" data-toggle="tab">pyLMM</a> </li> <li> - <a href="#rqtl_geno" data-toggle="tab">rqtl</a> + <a href="#rqtl_geno" data-toggle="tab">R/qtl</a> </li> <li> <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a> @@ -169,14 +169,14 @@ <input name="num_perm_reaper" value="2000" type="text" class="form-control"> </div> </div> - +<!-- <div class="mapping_method_fields form-group"> <label for="mapping_bootstraps" class="col-xs-2 control-label" title="Bootstrapping Resamples">Bootstrap</label> <div style="margin-left: 20px;" class="col-xs-4 controls"> <input name="mapping_bootstraps" value="2000" type="text" class="form-control"> </div> </div> - + <div class="mapping_method_fields form-group"> <label style="text-align:left;" class="col-xs-12 control-label">Display Additive Effect</label> <div class="col-xs-12 controls" id="display_additive_effect"> @@ -190,6 +190,7 @@ </label> </div> </div> +--> <div class="mapping_method_fields form-group"> <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label> |