diff options
| -rw-r--r--[-rwxr-xr-x] | wqflask/base/data_set.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 12 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 31 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait.html | 1 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_statistics.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 23 |
8 files changed, 68 insertions, 11 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 52ac95f0..053b45fc 100755..100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -417,6 +417,7 @@ class DataSet(object): self.shortname = None self.fullname = None self.type = None + self.data_scale = None #ZS: For example log2 self.setup() @@ -456,8 +457,8 @@ class DataSet(object): self.name, self.name)) - self.id, self.name, self.fullname, self.shortname, self.tissue = g.db.execute(""" - SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, Tissue.Name + self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = g.db.execute(""" + SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name FROM ProbeSetFreeze, ProbeFreeze, Tissue WHERE ProbeSetFreeze.public > %s AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index b56b179b..08f422f0 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -74,6 +74,8 @@ class MarkerRegression(object): 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.mapping_scale = "physic" + self.num_perm = 0 + self.perm_output = [] self.bootstrap_results = [] #ZS: This is passed to GN1 code for single chr mapping @@ -120,13 +122,14 @@ class MarkerRegression(object): try: if int(start_vars['num_perm']) > 0: self.num_perm = int(start_vars['num_perm']) - else: - self.num_perm = 0 except: self.num_perm = 0 self.LRSCheck = self.score_type - self.permCheck = "ON" + if self.num_perm > 0: + self.permCheck = "ON" + else: + self.permCheck = False self.showSNP = "ON" self.showGenes = "ON" self.viewLegend = "ON" @@ -273,6 +276,8 @@ class MarkerRegression(object): mapping_scale = self.mapping_scale, chromosomes = chromosome_mb_lengths, qtl_results = self.qtl_results, + num_perm = self.num_perm, + perm_results = self.perm_output, ) @@ -652,6 +657,7 @@ class MarkerRegression(object): self.perm_output = genotype.permutation(strains = trimmed_samples, trait = trimmed_values, nperm=self.num_perm) self.suggestive = self.perm_output[int(self.num_perm*0.37-1)] self.significant = self.perm_output[int(self.num_perm*0.95-1)] + self.highly_significant = self.perm_output[int(self.num_perm*0.99-1)] self.json_data['suggestive'] = self.suggestive self.json_data['significant'] = self.significant diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 79f1c867..074c78bf 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -150,6 +150,7 @@ class ShowTrait(object): self.trait_table_width = get_trait_table_width(self.sample_groups) js_data = dict(dataset_type = self.dataset.type, + data_scale = self.dataset.data_scale, sample_group_types = self.sample_group_types, sample_lists = sample_lists, attribute_names = self.sample_groups[0].attributes, diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 9d418e9b..9e249c28 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -190,9 +190,9 @@ } row_line = "<tr>"; if (row.url != null) { - row_line += "<td id=\"" + row.vn + "\" style=\"border-right: 1px solid #000000;\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>"; + row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>"; } else { - row_line += "<td id=\"" + row.vn + "\" style=\"border-right: 1px solid #000000;\">" + row.pretty + "</td>"; + row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>"; } _ref1 = js_data.sample_group_types; for (key in _ref1) { diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index 07f764ca..df948190 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -22,6 +22,7 @@ <input type="hidden" name="selected_chr" value="{{ selectedChr }}"> <input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}"> <input type="hidden" name="num_perm" value="{{ nperm }}"> + <input type="hidden" name="perm_results" value=""> <input type="hidden" name="num_bootstrap" value="{{ nboot }}"> <input type="hidden" name="do_control" value="{{ doControl }}"> <input type="hidden" name="control_marker" value="{{ controlLocus }}"> @@ -148,9 +149,12 @@ <br> <span style="white-space: nowrap;">A positive additive coefficient (green line) indicates that {{ dataset.group.parlist[1] }} alleles increase trait values. In contrast, a negative additive coefficient (orange line) indicates that {{ dataset.group.parlist[0] }} alleles increase trait values.</span> {% endif %} - {% if nperm > 0 %} + {% if nperm > 0 and permChecked == "ON" %} <br><br> <img src="/static/output/{{ perm_filename }}.gif"> + <br><br> + Total of {{ nperm }} permutations <a href="javascript:export_perm_data();" target="_blank" >Download Permutation Results</a> + <br> {% endif %} </div> </div> @@ -292,7 +296,20 @@ "scrollCollapse": true, "paging": false } ); - console.timeEnd("Creating table"); + + $('#interval_analyst').dataTable( { + "columnDefs": [ { + "targets": 0, + "sortable": false + }], + "order": [[3, "asc"]], + "sDom": "RZtir", + "iDisplayLength": -1, + "autoWidth": true, + "bDeferRender": true, + "bSortClasses": false, + "paging": false + } ); $('#vector_map_tab').click(function(){ $('div#gn1_map_options').hide(); @@ -325,6 +342,16 @@ return $('#marker_regression_form').submit(); }; + export_perm_data = function() { + var num_perm, perm_data; + num_perm = js_data.num_perm + perm_data = js_data.perm_results + json_perm_data = JSON.stringify(perm_data); + $('input[name=perm_results]').val(json_perm_data); + $('#marker_regression_form').attr('action', '/export_perm_data'); + return $('#marker_regression_form').submit(); + }; + </script> {% endblock %} diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 7429cd5f..64638fc7 100755 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -254,7 +254,6 @@ } ); {% endif %} - console.log("SAMPLE GROUP TYPES:", js_data.sample_group_types) if (Object.keys(js_data.sample_group_types).length > 1) { $('#stats_table').DataTable( { "columnDefs": [ diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 9a57b285..242f1c26 100755 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -26,7 +26,7 @@ <div class="tab-content"> <div class="tab-pane active" id="stats_tab"> <div style="padding: 20px" class="form-horizontal"> - <table id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped cell-border"></table> + <table border="1" id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped cell-border"></table> </div> </div> <div class="tab-pane" id="histogram_tab"> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 87ba8b32..bd2fff50 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -284,6 +284,29 @@ def export_trait_csv(): return Response(csv_data, mimetype='text/csv', headers={"Content-Disposition":"attachment;filename=sample_data.csv"}) + +@app.route('/export_perm_data', methods=('POST',)) +def export_perm_data(): + """CSV file consisting of the permutation data for the mapping results""" + num_perm = float(request.form['num_perm']) + perm_data = json.loads(request.form['perm_results']) + + buff = StringIO.StringIO() + writer = csv.writer(buff) + writer.writerow(["Suggestive LRS (p=0.63) = " + str(perm_data[int(num_perm*0.37-1)])]) + writer.writerow(["Significant LRS (p=0.05) = " + str(perm_data[int(num_perm*0.95-1)])]) + writer.writerow(["Highly Significant LRS (p=0.01) = " + str(perm_data[int(num_perm*0.99-1)])]) + writer.writerow("") + writer.writerow([str(num_perm) + " Permutations"]) + writer.writerow("") + for item in perm_data: + writer.writerow([item]) + csv_data = buff.getvalue() + buff.close() + + return Response(csv_data, + mimetype='text/csv', + headers={"Content-Disposition":"attachment;filename=perm_data.csv"}) @app.route("/show_trait") def show_trait_page(): |