diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 4 |
2 files changed, 12 insertions, 3 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 2d0ed1d7..bc8f8fd9 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -148,6 +148,7 @@ class DisplayMappingResults(object): self.this_trait = start_vars['this_trait'] self.n_samples = len(start_vars['vals']) self.species = start_vars['species'] + self.genofile_string = "" if 'genofile_string' in start_vars: self.genofile_string = start_vars['genofile_string'] @@ -887,7 +888,10 @@ class DisplayMappingResults(object): string1 = 'Dataset: %s' % (dataset_label) - string2 = 'Using Genotype File: %s' % self.genofile_string + if self.genofile_string == "": + string2 = 'Genotype File: %s.geno' % self.dataset.group.name + else: + string2 = 'Genotype File: %s' % self.genofile_string string4 = '' if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam": @@ -1852,7 +1856,10 @@ class DisplayMappingResults(object): Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max if self.manhattan_plot == True: - point_color = pid.black + if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1): + point_color = pid.grey + else: + point_color = pid.black canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=point_color, font=symbolFont) else: LRSCoordXY.append((Xc, Yc)) diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index d9cf50e2..3eb34d03 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -152,7 +152,7 @@ })(this)); //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping - var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', + var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', @@ -198,6 +198,7 @@ $('input[name=genofile]').val($('#genofile_gemma').val()); $('input[name=maf]').val($('input[name=maf_gemma]').val()); $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); return submit_special(url); }; @@ -218,6 +219,7 @@ $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')); $('input[name=suggestive]').val($('input[name=suggestive_reaper]')); $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); return submit_special(url); }; |