diff options
6 files changed, 101 insertions, 19 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 6a120325..63a7a555 100755 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -110,6 +110,17 @@ class CorrelationResults(object): self.min_expr = float(start_vars['min_expr']) self.p_range_lower = float(start_vars['p_range_lower']) self.p_range_upper = float(start_vars['p_range_upper']) + self.min_location_chr = start_vars['min_loc_chr'] + self.max_location_chr = start_vars['max_loc_chr'] + if start_vars['min_loc_mb'].isdigit(): + self.min_location_mb = start_vars['min_loc_mb'] + else: + self.min_location_mb = 0 + if start_vars['max_loc_mb'].isdigit(): + self.max_location_mb = start_vars['max_loc_mb'] + else: + self.max_location_mb = 1000 + self.max_location = [start_vars['max_loc_chr'], start_vars['max_loc_mb']] self.get_formatted_corr_type() self.return_number = int(start_vars['corr_return_results']) @@ -167,15 +178,35 @@ class CorrelationResults(object): key=lambda t: -abs(t[1][0]))) + #ZS: Convert min/max chromosome to an int for the location range option + min_chr_as_int = 1 + max_chr_as_int = 30 #Just to make sure all are included if user inputs nothing + for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): + if chr_info.name == self.min_location_chr: + min_chr_as_int = order_id + if chr_info.name == self.max_location_chr: + max_chr_as_int = order_id + for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]): print("trait name:", trait) trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True) - print("trait_object.mean:", trait_object.mean) - print("self.min_expr:", self.min_expr) - print("self.p_range_upper:", self.p_range_upper) + + #ZS: Convert trait chromosome to an int for the location range option + chr_as_int = 0 + for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): + if chr_info.name == trait_object.chr: + chr_as_int = order_id + if (float(trait_object.mean) > self.min_expr and float(self.correlation_data[trait][0]) > self.p_range_lower and - float(self.correlation_data[trait][0]) < self.p_range_upper): + float(self.correlation_data[trait][0]) < self.p_range_upper and + chr_as_int >= min_chr_as_int and + chr_as_int <= max_chr_as_int): + + if (chr_as_int == min_chr_as_int and float(trait_object.mb) < float(self.min_location_mb)): + continue + elif (chr_as_int == max_chr_as_int and float(trait_object.mb) > float(self.max_location_mb)): + continue (trait_object.sample_r, trait_object.sample_p, diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index e83437ab..850c99a7 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -139,9 +139,12 @@ class ShowTrait(object): self.temp_uuid = uuid.uuid4() self.sample_group_types = OrderedDict() - self.sample_group_types['samples_primary'] = self.dataset.group.name + " Only" - self.sample_group_types['samples_other'] = "Non-" + self.dataset.group.name - self.sample_group_types['samples_all'] = "All Cases" + if len(self.sample_groups) > 1: + self.sample_group_types['samples_primary'] = self.dataset.group.name + " Only" + self.sample_group_types['samples_other'] = "Non-" + self.dataset.group.name + self.sample_group_types['samples_all'] = "All Cases" + else: + self.sample_group_types['samples_primary'] = self.dataset.group.name sample_lists = [group.sample_list for group in self.sample_groups] print("sample_lists is:", pf(sample_lists)) diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 302d5ec4..1dd54e3a 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -179,13 +179,10 @@ for (key in _ref) { if (!__hasProp.call(_ref, key)) continue; value = _ref[key]; - console.log("aa key:", key); - console.log("aa value:", value); the_id = process_id("column", key); header += "<th id=\"" + the_id + "\">" + value + "</th>"; } header += "</thead>"; - console.log("windex header is:", header); the_rows = "<tbody>"; for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) { row = Stat_Table_Rows[_i]; @@ -201,9 +198,7 @@ for (key in _ref1) { if (!__hasProp.call(_ref1, key)) continue; value = _ref1[key]; - console.log("apple key:", key); the_id = process_id(key, row.vn); - console.log("the_id:", the_id); row_line += "<td id=\"" + the_id + "\">foo</td>"; } row_line += "</tr>"; diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index c5921ccf..a86a149d 100755 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -212,7 +212,7 @@ "buttons": [ 'csv' ], - "sDom": "RZBtir", + "sDom": "RZBtr", "iDisplayLength": -1, "autoWidth": false, "bLengthChange": true, @@ -240,7 +240,7 @@ "buttons": [ 'csv' ], - "sDom": "RZBtir", + "sDom": "RZBtr", "iDisplayLength": -1, "autoWidth": false, "bLengthChange": true, @@ -254,7 +254,48 @@ "paging": false } ); {% endif %} - + + console.log("SAMPLE GROUP TYPES:", js_data.sample_group_types) + if (Object.keys(js_data.sample_group_types).length > 1) { + $('#stats_table').DataTable( { + "columns": [ + { "bSortable": false }, + { "bSortable": false }, + { "bSortable": false }, + { "bSortable": false } + ], + "sDom": "RZtr", + "iDisplayLength": -1, + "autoWidth": false, + "bLengthChange": true, + "bDeferRender": true, + "bSortClasses": false, + "colResize": { + "tableWidthFixed": false + }, + "paging": false + } ); + } + else { + $('#stats_table').DataTable( { + "columns": [ + { "bSortable": false }, + { "bSortable": false } + ], + "sDom": "RZtr", + "iDisplayLength": -1, + "autoWidth": false, + "bLengthChange": true, + "bDeferRender": true, + "bSortClasses": false, + "colResize": { + "tableWidthFixed": false + }, + "paging": false + } ); + + } + var slider = document.getElementById('p_range_slider'); noUiSlider.create(slider, { start: [-1.0, 1.0], diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index cefe9763..65b9d08e 100755 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -80,6 +80,20 @@ </div> </div> <div class="form-group"> + <label class="col-xs-1 control-label">Location</label> + <div class="col-xs-4 controls"> + <span style="margin:10px;"> + Min Chr: <input name="min_loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;"> + Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> + </span> + <br> + <span style="margin:10px;"> + Max Chr: <input name="max_loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;"> + Mb: <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> + </span> + </div> + </div> + <div class="form-group"> <label class="col-xs-1 control-label">Range</label> <div class="col-xs-3 controls"> <input name="p_range_lower" value="" type="hidden"> diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html index b7323ba3..1932d968 100755 --- a/wqflask/wqflask/templates/show_trait_statistics_new.html +++ b/wqflask/wqflask/templates/show_trait_statistics_new.html @@ -24,10 +24,8 @@ <div class="tab-content"> <div class="tab-pane active" id="stats_tab"> <div style="padding: 20px" class="form-horizontal"> - <div class="well"> - <h3>Stats</h3> - <table id="stats_table" class="table table-hover"></table> - </div> + <table id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped"></table> + </div> </div> <div class="tab-pane" id="histogram_tab"> |