diff options
| -rw-r--r-- | wqflask/base/webqtlCaseData.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/SampleList.py | 19 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 40 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/css/show_trait.css | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js | 222 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 372 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 545 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/collections/view.html | 16 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 308 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_calculate_correlations.html | 12 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_mapping_tools.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_transform_and_filter.html | 145 |
13 files changed, 848 insertions, 865 deletions
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 2844cedd..3cf2d80d 100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -41,6 +41,8 @@ class webqtlCaseData: self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word) self.outlier = None # Not set to True/False until later + self.first_attr_col = self.get_first_attr_col() + def __repr__(self): case_data_string = "<webqtlCaseData> " if self.value is not None: @@ -79,3 +81,12 @@ class webqtlCaseData: if self.num_cases is not None: return "%s" % self.num_cases return "x" + + def get_first_attr_col(self): + col_num = 4 + if self.variance is not None: + col_num += 2 + if self.num_cases is not None: + col_num += 1 + + return col_num
\ No newline at end of file diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index dccd1ba8..e7676458 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -1,17 +1,13 @@ import re import itertools -import utility.logger from flask import g from base import webqtlCaseData +from pprint import pformat as pf from utility import Plot from utility import Bunch -from pprint import pformat as pf - -logger = utility.logger.getLogger(__name__) - class SampleList(object): def __init__(self, @@ -63,12 +59,15 @@ class SampleList(object): sample.this_id = str(counter) - # For extra attribute columns; currently only used by - # several datasets - Zach + # ZS: For extra attribute columns; currently only used by + # several datasets if self.sample_attribute_values: sample.extra_attributes = self.sample_attribute_values.get( sample_name, {}) + self.sample_list.append(sample) + + self.se_exists = any(sample.variance for sample in self.sample_list) self.do_outliers() def __repr__(self): @@ -149,12 +148,6 @@ class SampleList(object): attribute_values[self.attributes[item.Id].name] = attribute_value self.sample_attribute_values[sample_name] = attribute_values - def se_exists(self): - """Returns true if SE values exist for any samples, otherwise false""" - - return any(sample.variance for sample in self.sample_list) - - def natural_sort(list, key=lambda s: s): """ Sort the list into natural alphanumeric order. diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 88cd7dca..edf9638c 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -41,8 +41,6 @@ logger = getLogger(__name__ ) class ShowTrait(object): def __init__(self, kw): - logger.debug("in ShowTrait, kw are:", kw) - if 'trait_id' in kw and kw['dataset'] != "Temp": self.temp_trait = False self.trait_id = kw['trait_id'] @@ -150,6 +148,7 @@ class ShowTrait(object): #self.nearest_marker1 = "" #self.nearest_marker2 = "" + self.make_sample_lists() self.qnorm_vals = quantile_normalize_vals(self.sample_groups) @@ -273,7 +272,9 @@ class ShowTrait(object): data_scale = self.dataset.data_scale, sample_group_types = self.sample_group_types, sample_lists = sample_lists, - attribute_names = self.sample_groups[0].attributes, + se_exists = self.sample_groups[0].se_exists, + has_num_cases = self.has_num_cases, + attributes = self.sample_groups[0].attributes, categorical_vars = ",".join(categorical_var_list), num_values = self.num_values, qnorm_values = self.qnorm_vals, @@ -393,6 +394,7 @@ class ShowTrait(object): return_results_menu_selected = return_results_menu_selected,) def make_sample_lists(self): + all_samples_ordered = self.dataset.group.all_samples_ordered() parent_f1_samples = [] @@ -401,13 +403,19 @@ class ShowTrait(object): primary_sample_names = list(all_samples_ordered) + if not self.temp_trait: other_sample_names = [] + for sample in list(self.this_trait.data.keys()): - if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names): - primary_sample_names.append(self.this_trait.data[sample].name) - primary_sample_names.remove(self.this_trait.data[sample].name2) - elif sample not in all_samples_ordered: + if (self.this_trait.data[sample].name2 != self.this_trait.data[sample].name): + if ((self.this_trait.data[sample].name2 in primary_sample_names) and + (self.this_trait.data[sample].name not in primary_sample_names)): + primary_sample_names.append(self.this_trait.data[sample].name) + primary_sample_names.remove(self.this_trait.data[sample].name2) + + all_samples_set = set(all_samples_ordered) + if sample not in all_samples_set: all_samples_ordered.append(sample) other_sample_names.append(sample) @@ -420,6 +428,7 @@ class ShowTrait(object): primary_header = "%s Only" % (self.dataset.group.name) else: primary_header = "Samples" + primary_samples = SampleList(dataset = self.dataset, sample_names=primary_sample_names, this_trait=self.this_trait, @@ -452,6 +461,7 @@ class ShowTrait(object): self.primary_sample_names = primary_sample_names self.dataset.group.allsamples = all_samples_ordered + def quantile_normalize_vals(sample_groups): def normf(trait_vals): ranked_vals = ss.rankdata(trait_vals) @@ -490,6 +500,7 @@ def quantile_normalize_vals(sample_groups): return qnorm_by_group + def get_z_scores(sample_groups): zscore_by_group = [] for sample_type in sample_groups: @@ -514,11 +525,10 @@ def get_z_scores(sample_groups): return zscore_by_group + def get_nearest_marker(this_trait, this_db): this_chr = this_trait.locus_chr - logger.debug("this_chr:", this_chr) this_mb = this_trait.locus_mb - logger.debug("this_mb:", this_mb) #One option is to take flanking markers, another is to take the two (or one) closest query = """SELECT Geno.Name FROM Geno, GenoXRef, GenoFreeze @@ -529,7 +539,6 @@ def get_nearest_marker(this_trait, this_db): ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name+"Geno", this_mb) logger.sql(query) result = g.db.execute(query).fetchall() - logger.debug("result:", result) if result == []: return "" @@ -537,13 +546,14 @@ def get_nearest_marker(this_trait, this_db): else: return result[0][0] + def get_table_widths(sample_groups, has_num_cases=False): stats_table_width = 250 if len(sample_groups) > 1: stats_table_width = 450 trait_table_width = 380 - if sample_groups[0].se_exists(): + if sample_groups[0].se_exists: trait_table_width += 80 if has_num_cases: trait_table_width += 80 @@ -553,6 +563,7 @@ def get_table_widths(sample_groups, has_num_cases=False): return stats_table_width, trait_table_width + def has_num_cases(this_trait): has_n = False if this_trait.dataset.type != "ProbeSet" and this_trait.dataset.type != "Geno": @@ -563,6 +574,7 @@ def has_num_cases(this_trait): return has_n + def get_trait_units(this_trait): unit_type = "" inside_brackets = False @@ -582,6 +594,7 @@ def get_trait_units(this_trait): return unit_type + def check_if_attr_exists(the_trait, id_type): if hasattr(the_trait, id_type): if getattr(the_trait, id_type) == None or getattr(the_trait, id_type) == "": @@ -591,6 +604,7 @@ def check_if_attr_exists(the_trait, id_type): else: return False + def get_ncbi_summary(this_trait): if check_if_attr_exists(this_trait, 'geneid'): #ZS: Need to switch this try/except to something that checks the output later @@ -603,6 +617,7 @@ def get_ncbi_summary(this_trait): else: return None + def get_categorical_variables(this_trait, sample_list): categorical_var_list = [] @@ -621,6 +636,7 @@ def get_categorical_variables(this_trait, sample_list): return categorical_var_list + def get_genotype_scales(genofiles): geno_scales = {} if isinstance(genofiles, list): @@ -632,6 +648,7 @@ def get_genotype_scales(genofiles): return geno_scales + def get_scales_from_genofile(file_location): geno_path = locate_ignore_error(file_location, 'genotype') @@ -684,6 +701,7 @@ def get_scales_from_genofile(file_location): if i > first_marker_line + 10: break + #ZS: This assumes that both won't be all zero, since if that's the case mapping shouldn't be an option to begin with if mb_all_zero: return [["morgan", "cM"]] diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 92deab20..7a7f5455 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -48,6 +48,13 @@ table.dataTable.cell-border tbody tr td:first-child { border-left: 1px solid #ccc; } +.checkbox { + min-height: 20px; +} + +.trait_value_input { + text-align: right; + .glyphicon { position: relative; top: 2px; diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js new file mode 100644 index 00000000..97b71306 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js @@ -0,0 +1,222 @@ +// ZS: This file initializes the tables for the show_trait page + +// ZS: This variable is just created to get the column position of the first case attribute (if case attributes exist), since it's needed to set the row classes in createdRow for the DataTable +var attribute_start_pos = 3; +if (js_data.se_exists) { + attribute_start_pos += 2; +} +if (js_data.has_num_cases === true) { + attribute_start_post += 1; +} + +build_columns = function() { + let column_list = [ + { + 'data': null, + 'orderDataType': "dom-checkbox", + 'searchable' : false, + 'render': function(data, type, row, meta) { + return '<input type="checkbox" name="searchResult" class="checkbox edit_sample_checkbox" value="">' + } + }, + { + 'title': "ID", + 'type': "natural", + 'searchable' : false, + 'data': "this_id" + }, + { + 'title': "Sample", + 'type': "natural", + 'data': null, + 'render': function(data, type, row, meta) { + return '<span class="edit_sample_sample_name">' + data.name + '</span>' + } + }, + { + 'title': "<div style='text-align: right;'>Value</div>", + 'orderDataType': "dom-input", + 'type': "cust-txt", + 'data': null, + 'render': function(data, type, row, meta) { + if (data.value == null) { + return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>' + } else { + return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>' + } + } + } + ]; + + if (js_data.se_exists) { + column_list.push( + { + 'bSortable': false, + 'type': "natural", + 'data': null, + 'searchable' : false, + 'render': function(data, type, row, meta) { + return '±' + } + }, + { + 'title': "<div style='text-align: right;'>SE</div>", + 'orderDataType': "dom-input", + 'type': "cust-txt", + 'data': null, + 'render': function(data, type, row, meta) { + if (data.variance == null) { + return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>' + } else { + return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>' + } + } + } + ); + } + + if (js_data.has_num_cases === "true") { + column_list.push( + { + 'title': "<div style='text-align: right;'>N</div>", + 'orderDataType': "dom-input", + 'type': "cust-txt", + 'data': null, + 'render': function(data, type, row, meta) { + if (data.num_cases == null || data.num_cases == undefined) { + return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>' + } else { + return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>' + } + } + } + ); + } + + attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name > js_data.attributes[b].name) ? 1 : -1) + for (i = 0; i < attr_keys.length; i++){ + column_list.push( + { + 'title': "<div style='text-align: " + js_data.attributes[attr_keys[i]].alignment + "'>" + js_data.attributes[attr_keys[i]].name + "</div>", + 'type': "natural", + 'data': null, + 'render': function(data, type, row, meta) { + attr_name = Object.keys(data.extra_attributes).sort((a, b) => (a > b) ? 1 : -1)[meta.col - data.first_attr_col] + if (attr_name != null && attr_name != undefined){ + return data.extra_attributes[attr_name] + } else { + return "" + } + } + } + ) + } + + return column_list +} + +var primary_table = $('#samples_primary').DataTable( { + 'initComplete': function(settings, json) { + $('.edit_sample_value').change(function() { + edit_data_change(); + }); + }, + 'createdRow': function ( row, data, index ) { + $(row).attr('id', "Primary_" + data.this_id) + $(row).addClass("value_se"); + if (data.outlier) { + $(row).addClass("outlier"); + } + $('td', row).eq(1).addClass("column_name-Index") + $('td', row).eq(2).addClass("column_name-Sample") + $('td', row).eq(3).addClass("column_name-Value") + if (js_data.se_exists) { + $('td', row).eq(5).addClass("column_name-SE") + if (js_data.has_num_cases === "true") { + $('td', row).eq(6).addClass("column_name-num_cases") + } else { + if (js_data.has_num_cases === "true") { + $('td', row).eq(4).addClass("column_name-num_cases") + } + } + } else { + if (js_data.has_num_cases === "true") { + $('td', row).eq(4).addClass("column_name-num_cases") + } + } + + sorted_key_list = Object.keys(js_data.attributes).sort() + for (i=0; i < sorted_key_list.length; i++) { + $('td', row).eq(attribute_start_pos + i + 1).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name) + $('td', row).eq(attribute_start_pos + i + 1).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;") + } + }, + 'data': js_data['sample_lists'][0], + 'columns': build_columns(), + 'order': [[1, "asc"]], + 'sDom': "Ztr", + 'autoWidth': true, + 'orderClasses': true, + "scrollY": "50vh", + 'scroller': true, + 'scrollCollapse': true +} ); + +primary_table.on( 'order.dt search.dt draw.dt', function () { + primary_table.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) { + cell.innerHTML = i+1; + } ); +} ).draw(); + +$('#primary_searchbox').on( 'keyup', function () { + primary_table.search($(this).val()).draw(); +} ); + +if (js_data.sample_lists.length > 1){ + var other_table = $('#samples_other').DataTable( { + 'initComplete': function(settings, json) { + $('.edit_sample_value').change(function() { + edit_data_change(); + }); + }, + 'createdRow': function ( row, data, index ) { + $(row).attr('id', "Primary_" + data.this_id) + $(row).addClass("value_se"); + if (data.outlier) { + $(row).addClass("outlier"); + } + $('td', row).eq(1).addClass("column_name-Index") + $('td', row).eq(2).addClass("column_name-Sample") + $('td', row).eq(3).addClass("column_name-Value") + if (js_data.se_exists) { + $('td', row).eq(5).addClass("column_name-SE") + if (js_data.has_num_cases === "true") { + $('td', row).eq(6).addClass("column_name-num_cases") + } else { + if (js_data.has_num_cases === "true") { + $('td', row).eq(4).addClass("column_name-num_cases") + } + } + } else { + if (js_data.has_num_cases === "true") { + $('td', row).eq(4).addClass("column_name-num_cases") + } + } + + sorted_key_list = Object.keys(js_data.attributes).sort() + for (i=0; i < sorted_key_list.length; i++) { + $('td', row).eq(attribute_start_pos + i + 1).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name) + $('td', row).eq(attribute_start_pos + i + 1).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;") + } + }, + 'data': js_data['sample_lists'][1], + 'columns': build_columns(), + 'order': [[1, "asc"]], + 'sDom': "Ztr", + 'autoWidth': true, + 'orderClasses': true, + "scrollY": "50vh", + 'scroller': true, + 'scrollCollapse': true + } ); +}
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index c0784073..eaad0a4c 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -440,38 +440,47 @@ edit_data_change = function() { samples_other: {}, samples_all: {} }; + tables = ['samples_primary', 'samples_other']; for (_i = 0, _len = tables.length; _i < _len; _i++) { table = tables[_i]; - rows = $("#" + table).find('tr'); - for (_j = 0, _len1 = rows.length; _j < _len1; _j++) { - row = rows[_j]; - name = $(row).find('.edit_sample_sample_name').html(); - name = $.trim(name); - real_value = $(row).find('.edit_sample_value').val(); - checkbox = $(row).find(".edit_sample_checkbox"); - if (is_number(real_value) && real_value !== "") { - real_value = parseFloat(real_value); - sample_sets[table].add_value(real_value); - real_variance = $(row).find('.edit_sample_se').val(); - if (is_number(real_variance)) { - real_variance = parseFloat(real_variance); - } else { - real_variance = null; - } - real_dict = { - value: real_value, - variance: real_variance - }; - root.selected_samples[table][name] = real_dict; - if (!(name in already_seen)) { - sample_sets['samples_all'].add_value(real_value); - root.selected_samples['samples_all'][name] = real_dict; - already_seen[name] = true; + if ($('#' + table).length){ + table_api = $('#' + table).DataTable(); + sample_vals = []; + name_nodes = table_api.column(2).nodes().to$(); + val_nodes = table_api.column(3).nodes().to$(); + var_nodes = table_api.column(5).nodes().to$(); + for (_j = 0; _j < val_nodes.length; _j++){ + sample_val = val_nodes[_j].childNodes[0].value + sample_name = $.trim(name_nodes[_j].childNodes[0].textContent) + if (is_number(sample_val) && sample_val !== "") { + sample_val = parseFloat(sample_val); + sample_sets[table].add_value(sample_val); + if (typeof var_nodes !== 'undefined'){ + sample_var = null; + } else { + sample_var = var_nodes[_j].childNodes[0].value + if (is_number(sample_var)) { + sample_var = parseFloat(sample_var) + } else { + sample_var = null; + } + } + sample_dict = { + value: sample_val, + variance: sample_var + } + root.selected_samples[table][sample_name] = sample_dict; + if (!(sample_name in already_seen)) { + sample_sets['samples_all'].add_value(sample_val); + root.selected_samples['samples_all'][sample_name] = sample_dict; + already_seen[sample_name] = true; + } } } } } + update_stat_values(sample_sets); if ($('#histogram').hasClass('js-plotly-plot')){ @@ -490,6 +499,7 @@ edit_data_change = function() { return update_prob_plot(); } }; + show_hide_outliers = function() { var label; label = $('#show_hide_outliers').val(); @@ -500,6 +510,7 @@ show_hide_outliers = function() { return console.log("Should be now Hide Outliers"); } }; + on_corr_method_change = function() { var corr_method; corr_method = $('select[name=corr_type]').val(); @@ -514,10 +525,30 @@ on_corr_method_change = function() { $('select[name=corr_type]').change(on_corr_method_change); submit_special = function(url) { + get_table_contents_for_form_submit("trait_data_form"); $("#trait_data_form").attr("action", url); $("#trait_data_form").submit(); }; +get_table_contents_for_form_submit = function(form_id) { + // Borrowed code from - https://stackoverflow.com/questions/31418047/how-to-post-data-for-the-whole-table-using-jquery-datatables + let this_form = $("#" + form_id); + var params = primary_table.$('input').serializeArray(); + + $.each(params, function(){ + // If element doesn't exist in DOM + if(!$.contains(document, this_form[this.name])){ + // Create a hidden element + this_form.append( + $('<input>') + .attr('type', 'hidden') + .attr('name', this.name) + .val(this.value) + ); + } + }); +} + var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr', 'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper'] @@ -538,10 +569,9 @@ populate_sample_attributes_values_dropdown = function() { var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results; $('#attribute_values').empty(); sample_attributes = {}; - _ref = js_data.attribute_names; - for (key in _ref) { - if (!__hasProp.call(_ref, key)) continue; - attribute_info = _ref[key]; + attr_keys = Object.keys(js_data.attributes).sort(); + for (i=0; i < attr_keys.length; i++) { + attribute_info = js_data.attributes[attr_keys[i]]; sample_attributes[attribute_info.name] = attribute_info.distinct_values; } selected_attribute = $('#exclude_menu').val().replace("_", " "); @@ -549,13 +579,17 @@ populate_sample_attributes_values_dropdown = function() { _results = []; for (_i = 0, _len = _ref1.length; _i < _len; _i++) { value = _ref1[_i]; - _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values'))); + if (value != ""){ + _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values'))); + } } return _results; }; -if (Object.keys(js_data.attribute_names).length > 0) { + +if (Object.keys(js_data.attributes).length){ populate_sample_attributes_values_dropdown(); } + $('#exclude_menu').change(populate_sample_attributes_values_dropdown); block_by_attribute_value = function() { var attribute_name, cell_class, exclude_by_value; @@ -580,20 +614,6 @@ block_by_index = function() { _ref = index_string.split(","); for (_i = 0, _len = _ref.length; _i < _len; _i++) { index_set = _ref[_i]; - /* - if (index_set.indexOf('<') !== -1) { - try { - start_index = parseInt(index_set.split("<")[0]); - end_index = parseInt(index_set.split("<")[1]); - for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) { - index_list.push(index); - } - } catch (_error) { - error = _error; - alert("Syntax error"); - } - } - */ if (index_set.indexOf('-') !== -1) { try { start_index = parseInt(index_set.split("-")[0]); @@ -611,19 +631,18 @@ block_by_index = function() { } } _results = []; + let block_group = $('#block_group').val(); + if (block_group === "other") { + table_api = $('#samples_other').DataTable(); + } else { + table_api = $('#samples_primary').DataTable(); + } + val_nodes = table_api.column(3).nodes().to$(); for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) { index = index_list[_k]; - if ($('#block_group').val() === "primary") { - _results.push($('#samples_primary').find('td.column_name-Index').filter(function() { return $(this).text() == index.toString() }).closest('tr').find('.trait_value_input').val("x")); - } else if ($('#block_group').val() === "other") { - _results.push($('#samples_other').find('td.column_name-Index').filter(function() { return $(this).text() == index.toString() }).closest('tr').find('.trait_value_input').val("x")); - } else { - _results.push(void 0); - } + val_nodes[index - 1].childNodes[0].value = "x"; } - return _results; }; -$('#block_by_index').click(block_by_index); hide_no_value = function() { return $('.value_se').each((function(_this) { @@ -635,6 +654,7 @@ hide_no_value = function() { })(this)); }; $('#hide_no_value').click(hide_no_value); + block_outliers = function() { return $('.outlier').each((function(_this) { return function(_index, element) { @@ -643,177 +663,195 @@ block_outliers = function() { })(this)); }; $('#block_outliers').click(block_outliers); + reset_samples_table = function() { $('input[name="transform"]').val(""); $('span[name="transform_text"]').text("") - return $('.trait_value_input').each((function(_this) { - return function(_index, element) { - $(element).val($(element).data('value')); - return $(element).parents('.value_se').show(); - }; - })(this)); + + tables = ['samples_primary', 'samples_other']; + for (_i = 0, _len = tables.length; _i < _len; _i++) { + table = tables[_i]; + if ($('#' + table).length) { + table_api = $('#' + table).DataTable(); + val_nodes = table_api.column(3).nodes().to$(); + for (i = 0; i < val_nodes.length; i++) { + this_node = val_nodes[i].childNodes[0]; + this_node.value = this_node.attributes["data-value"].value; + } + if (js_data.se_exists){ + se_nodes = table_api.column(5).nodes().to$(); + for (i = 0; i < val_nodes.length; i++) { + this_node = val_nodes[i].childNodes[0]; + this_node.value = this_node.attributes["data-value"].value; + } + } + } + } }; $('.reset').click(function() { reset_samples_table(); edit_data_change(); }); -log2_normalize_data = function(zero_to_one_vals_exist) { - return $('.trait_value_input').each((function(_this) { - return function(_index, element) { - current_value = $(element).data("value") - if(isNaN(current_value)) { - return current_value - } else { - if (zero_to_one_vals_exist){ - current_value = parseFloat(current_value) + 1; +check_for_zero_to_one_vals = function() { + tables = ['samples_primary', 'samples_other']; + for (_i = 0, _len = tables.length; _i < _len; _i++) { + table = tables[_i]; + if ($('#' + table).length) { + table_api = $('#' + table).DataTable(); + val_nodes = table_api.column(3).nodes().to$(); + for (i = 0; i < val_nodes.length; i++) { + this_node = val_nodes[i].childNodes[0]; + if(!isNaN(this_node.value)) { + if (0 <= this_node.value && this_node.value < 1){ + return true + } } - $(element).val(Math.log2(current_value).toFixed(3)); - return Math.log2(current_value).toFixed(3) } - }; - })(this)); -}; + } + } + return false +} -log10_normalize_data = function(zero_to_one_vals_exist) { - return $('.trait_value_input').each((function(_this) { - return function(_index, element) { - current_value = $(element).data("value") - if(isNaN(current_value)) { - return current_value - } else { - if (zero_to_one_vals_exist){ - current_value = parseFloat(current_value) + 1; - } - $(element).val(Math.log10(current_value).toFixed(3)); - return Math.log10(current_value).toFixed(3) - } - }; - })(this)); +log2_data = function(this_node) { + current_value = this_node.value; + original_value = this_node.attributes['data-value'].value; + if(!isNaN(current_value) && !isNaN(original_value)) { + if (zero_to_one_vals_exist){ + original_value = parseFloat(original_value) + 1; + } + this_node.value = Math.log2(original_value).toFixed(3); + } }; +log10_data = function() { + current_value = this_node.value; + original_value = this_node.attributes['data-value'].value; + if(!isNaN(current_value) && !isNaN(original_value)) { + if (zero_to_one_vals_exist){ + original_value = parseFloat(original_value) + 1; + } + this_node.value = Math.log10(original_value).toFixed(3); + } +}; -sqrt_normalize_data = function() { - return $('.edit_sample_value').each((function(_this) { - return function(_index, element) { - current_value = parseFloat($(element).data("value")) + 1; - if(isNaN(current_value)) { - return current_value - } else { - $(element).val(Math.sqrt(current_value).toFixed(3)); - return Math.sqrt(current_value).toFixed(3) - } - }; - })(this)); +sqrt_data = function() { + current_value = this_node.value; + original_value = this_node.attributes['data-value'].value; + if(!isNaN(current_value) && !isNaN(original_value)) { + if (zero_to_one_vals_exist){ + original_value = parseFloat(original_value) + 1; + } + this_node.value = Math.sqrt(original_value).toFixed(3); + } }; invert_data = function() { - return $('.edit_sample_value').each((function(_this) { - return function(_index, element) { - current_value = parseFloat($(element).val()); - if(isNaN(current_value)) { - return current_value - } else { - $(element).val(-(current_value)); - return -(current_value) - } - }; - })(this)); + current_value = this_node.value; + if(!isNaN(current_value)) { + this_node.value = parseFloat(-(current_value)).toFixed(3); + } }; - qnorm_data = function() { - return $('.edit_sample_value').each((function(_this) { - return function(_index, element) { - current_value = parseFloat($(element).data("value")) + 1; - if(isNaN(current_value)) { - return current_value - } else { - $(element).val($(element).data("qnorm")); - return $(element).data("qnorm"); - } - }; - })(this)); + current_value = this_node.value; + qnorm_value = this_node.attributes['data-qnorm'].value; + if(!isNaN(current_value)) { + this_node.value = qnorm_value; + } }; zscore_data = function() { - return $('.edit_sample_value').each((function(_this) { - return function(_index, element) { - current_value = parseFloat($(element).data("value")) + 1; - if(isNaN(current_value)) { - return current_value - } else { - $(element).val($(element).data("zscore")); - return $(element).data("zscore"); - } - }; - })(this)); + current_value = this_node.value; + zscore_value = this_node.attributes['data-zscore'].value; + if(!isNaN(current_value)) { + this_node.value = zscore_value; + } }; -check_for_zero_to_one_vals = function() { - zero_to_one_vals_exist = false - $('.trait_value_input').each(function() { - current_value = $(this).data("value") - if(isNaN(current_value)) { - return true; - } else { - current_value = parseFloat(current_value) - if (0 <= current_value && current_value < 1){ - zero_to_one_vals_exist = true - return false +do_transform = function(transform_type) { + tables = ['samples_primary', 'samples_other']; + for (_i = 0, _len = tables.length; _i < _len; _i++) { + table = tables[_i]; + if ($('#' + table).length) { + table_api = $('#' + table).DataTable(); + val_nodes = table_api.column(3).nodes().to$(); + for (i = 0; i < val_nodes.length; i++) { + this_node = val_nodes[i].childNodes[0] + if (transform_type == "log2"){ + log2_data(this_node) + } + if (transform_type == "log10"){ + log10_data(this_node) + } + if (transform_type == "sqrt"){ + sqrt_data(this_node) + } + if (transform_type == "invert"){ + invert_data(this_node) + } + if (transform_type == "qnorm"){ + qnorm_data(this_node) + } + if (transform_type == "zscore"){ + zscore_data(this_node) + } } } - }); - return zero_to_one_vals_exist + } } normalize_data = function() { if ($('#norm_method option:selected').val() == 'log2' || $('#norm_method option:selected').val() == 'log10'){ if ($('input[name="transform"]').val() != "log2" && $('#norm_method option:selected').val() == 'log2') { - log2_normalize_data(zero_to_one_vals_exist) + do_transform("log2") $('input[name="transform"]').val("log2") - $('span[name="transform_text"]').text(" - log2 transformed") + $('span[name="transform_text"]').text(" - log2 Transformed") } else { if ($('input[name="transform"]').val() != "log10" && $('#norm_method option:selected').val() == 'log10'){ - log10_normalize_data(zero_to_one_vals_exist) + do_transform("log10") $('input[name="transform"]').val("log10") - $('span[name="transform_text"]').text(" - log10 transformed") + $('span[name="transform_text"]').text(" - log10 Transformed") } } } else if ($('#norm_method option:selected').val() == 'sqrt'){ if ($('input[name="transform"]').val() != "sqrt") { - sqrt_normalize_data() + do_transform("sqrt") $('input[name="transform"]').val("sqrt") - $('span[name="transform_text"]').text(" - Square Root transformed") + $('span[name="transform_text"]').text(" - Square Root Transformed") } } else if ($('#norm_method option:selected').val() == 'invert'){ - invert_data() + do_transform("invert") $('input[name="transform"]').val("inverted") - $('span[name="transform_text"]').text(" - Inverted") + if ($('span[name="transform_text"]:eq(0)').text() != ""){ + current_text = $('span[name="transform_text"]:eq(0)').text(); + $('span[name="transform_text"]').text(current_text + " and Inverted"); + } else { + $('span[name="transform_text"]').text(" - Inverted") + } } else if ($('#norm_method option:selected').val() == 'qnorm'){ if ($('input[name="transform"]').val() != "qnorm") { - qnorm_data() + do_transform("qnorm") $('input[name="transform"]').val("qnorm") $('span[name="transform_text"]').text(" - Quantile Normalized") } } else if ($('#norm_method option:selected').val() == 'zscore'){ if ($('input[name="transform"]').val() != "zscore") { - zscore_data() + do_transform("zscore") $('input[name="transform"]').val("zscore") $('span[name="transform_text"]').text(" - Z-Scores") } } } -zero_to_one_vals_exist = false +zero_to_one_vals_exist = check_for_zero_to_one_vals(); show_transform_warning = function() { transform_type = $('#norm_method option:selected').val() - zero_to_one_vals_exist = check_for_zero_to_one_vals(); if (transform_type == "log2" || transform_type == "log10"){ if (zero_to_one_vals_exist){ $('#transform_alert').css("display", "block") @@ -859,10 +897,9 @@ get_sample_table_data = function(table_name) { if ($(element).find('.edit_sample_num_cases').length > 0) { row_data.num_cases = $(element).find('.edit_sample_num_cases').val(); } - _ref = js_data.attribute_names; - for (key in _ref) { - if (!__hasProp.call(_ref, key)) continue; - attribute_info = _ref[key]; + attr_keys = Object.keys(js_data.attributes).sort() + for (i=0; i < attr_keys.length; i++) { + attribute_info = js_data.attributes[attr_keys[i]]; row_data[attribute_info.name] = $.trim($(element).find('.column_name-' + attribute_info.name.replace(" ", "_").replace("/", "\\/")).text()); } return samples.push(row_data); @@ -1447,8 +1484,11 @@ $('.stats_panel').click(function() { edit_data_change(); } }); -$('#edit_sample_lists').change(edit_data_change); -$('#block_by_index').click(edit_data_change); + +$('#block_by_index').click(function(){ + block_by_index(); + edit_data_change(); +}); $('#exclude_group').click(edit_data_change); $('#block_outliers').click(edit_data_change); $('#reset').click(edit_data_change); 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 4dce0705..c0f36eaa 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -1,307 +1,298 @@ -// Generated by CoffeeScript 1.8.0 -(function() { - var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining; +var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining; - submit_special = function(url) { - $("#trait_data_form").attr("action", url); - $("#trait_data_form").submit(); - }; - - update_time_remaining = function(percent_complete) { - var minutes_remaining, now, period, total_seconds_remaining; - now = new Date(); - period = now.getTime() - root.start_time; - console.log("period is:", period); - if (period > 8000) { - total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000; - minutes_remaining = Math.round(total_seconds_remaining / 60); - if (minutes_remaining < 3) { - return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining"); - } else { - return $('#time_remaining').text(minutes_remaining + " minutes remaining"); - } +update_time_remaining = function(percent_complete) { + var minutes_remaining, now, period, total_seconds_remaining; + now = new Date(); + period = now.getTime() - root.start_time; + console.log("period is:", period); + if (period > 8000) { + total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000; + minutes_remaining = Math.round(total_seconds_remaining / 60); + if (minutes_remaining < 3) { + return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining"); + } else { + return $('#time_remaining').text(minutes_remaining + " minutes remaining"); } - }; + } +}; - get_progress = function() { - var params, params_str, temp_uuid, url; - console.log("temp_uuid:", $("#temp_uuid").val()); - temp_uuid = $("#temp_uuid").val(); - params = { - key: temp_uuid - }; - params_str = $.param(params); - url = "/get_temp_data?" + params_str; - console.log("url:", url); - $.ajax({ - type: "GET", - url: url, - success: (function(_this) { - return function(progress_data) { - var percent_complete; - percent_complete = progress_data['percent_complete']; - console.log("in get_progress data:", progress_data); - $('#marker_regression_progress').css("width", percent_complete + "%"); - if (root.start_time) { - if (!isNaN(percent_complete)) { - return update_time_remaining(percent_complete); - } - } else { - return root.start_time = new Date().getTime(); - } - }; - })(this) - }); - return false; +get_progress = function() { + var params, params_str, temp_uuid, url; + console.log("temp_uuid:", $("#temp_uuid").val()); + temp_uuid = $("#temp_uuid").val(); + params = { + key: temp_uuid }; - - block_outliers = function() { - return $('.outlier').each((function(_this) { - return function(_index, element) { - return $(element).find('.trait_value_input').val('x'); + params_str = $.param(params); + url = "/get_temp_data?" + params_str; + console.log("url:", url); + $.ajax({ + type: "GET", + url: url, + success: (function(_this) { + return function(progress_data) { + var percent_complete; + percent_complete = progress_data['percent_complete']; + console.log("in get_progress data:", progress_data); + $('#marker_regression_progress').css("width", percent_complete + "%"); + if (root.start_time) { + if (!isNaN(percent_complete)) { + return update_time_remaining(percent_complete); + } + } else { + return root.start_time = new Date().getTime(); + } }; - })(this)); - }; - - do_ajax_post = function(url, form_data) { - $.ajax({ - type: "POST", - url: url, - data: form_data, - error: (function(_this) { - return function(xhr, ajaxOptions, thrownError) { - alert("Sorry, an error occurred"); - console.log(xhr); - clearInterval(_this.my_timer); - $('#progress_bar_container').modal('hide'); - $('#static_progress_bar_container').modal('hide'); - return $("body").html("We got an error."); - }; - })(this), - success: (function(_this) { - return function(data) { - clearInterval(_this.my_timer); - $('#progress_bar_container').modal('hide'); - $('#static_progress_bar_container').modal('hide'); - return open_mapping_results(data); - }; - })(this) - }); - console.log("settingInterval"); - this.my_timer = setInterval(get_progress, 1000); - return false; - }; - - open_mapping_results = function(data) { - return $.colorbox({ - html: data, - href: "#mapping_results_holder", - height: "90%", - width: "90%", - onComplete: (function(_this) { - return function() { - var filename, getSvgXml; - root.create_lod_chart(); - filename = "lod_chart_" + js_data.this_trait; - getSvgXml = function() { - var svg; - svg = $("#topchart").find("svg")[0]; - return (new XMLSerializer).serializeToString(svg); - }; - $("#exportform > #export").click(function() { - var form, svg_xml; - svg_xml = getSvgXml(); - form = $("#exportform"); - form.find("#data").val(svg_xml); - form.find("#filename").val(filename); - return form.submit(); - }); - return $("#exportpdfform > #export_pdf").click(function() { - var form, svg_xml; - svg_xml = getSvgXml(); - form = $("#exportpdfform"); - form.find("#data").val(svg_xml); - form.find("#filename").val(filename); - return form.submit(); - }); - }; - })(this) - }); - }; - - outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results."; - showalert = function(message, alerttype) { - return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>'); - }; - - $('#suggestive').hide(); + })(this) + }); + return false; +}; - $('input[name=display_all]').change((function(_this) { - return function() { - console.log("check"); - if ($('input[name=display_all]:checked').val() === "False") { - return $('#suggestive').show(); - } else { - return $('#suggestive').hide(); - } +block_outliers = function() { + return $('.outlier').each((function(_this) { + return function(_index, element) { + return $(element).find('.trait_value_input').val('x'); }; })(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', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', - 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', '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', - 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples'] - - $(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) { - return function() { - if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){ - var form_data, url; - url = "/loading"; - $('input[name=method]').val("rqtl_geno"); - $('input[name=selected_chr]').val($('#chr_rqtl_geno').val()); - $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val()); - $('input[name=genofile]').val($('#genofile_rqtl_geno').val()); - $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val()); - $('input[name=categorical_vars]').val(js_data.categorical_vars) - $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val()); - $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val()); - $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').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); - } else { - return true - } - }; - })(this)); - - $(".gemma_tab, #gemma_compute").on("click", (function(_this) { - return function() { - if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){ - var form_data, url; - console.log("RUNNING GEMMA"); - url = "/loading"; - $('input[name=method]').val("gemma"); - $('input[name=selected_chr]').val($('#chr_gemma').val()); - $('input[name=num_perm]').val(0); - $('input[name=genofile]').val($('#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); - } else { - return true - } - }; - })(this)); +do_ajax_post = function(url, form_data) { + $.ajax({ + type: "POST", + url: url, + data: form_data, + error: (function(_this) { + return function(xhr, ajaxOptions, thrownError) { + alert("Sorry, an error occurred"); + console.log(xhr); + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + $('#static_progress_bar_container').modal('hide'); + return $("body").html("We got an error."); + }; + })(this), + success: (function(_this) { + return function(data) { + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + $('#static_progress_bar_container').modal('hide'); + return open_mapping_results(data); + }; + })(this) + }); + console.log("settingInterval"); + this.my_timer = setInterval(get_progress, 1000); + return false; +}; - $(".reaper_tab, #interval_mapping_compute").on("click", (function(_this) { - return function() { - if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){ - var form_data, url; - console.log("In interval mapping"); - url = "/loading"; - $('input[name=method]').val("reaper"); - $('input[name=selected_chr]').val($('#chr_reaper').val()); - $('input[name=mapping_scale]').val($('#scale_reaper').val()); - $('input[name=genofile]').val($('#genofile_reaper').val()); - $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val()); - $('input[name=control_marker]').val($('input[name=control_reaper]').val()); - $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val()); - $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val()); - $('input[name=mapping_display_all]').val($('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); - } else { - return true - } - }; - })(this)); +open_mapping_results = function(data) { + return $.colorbox({ + html: data, + href: "#mapping_results_holder", + height: "90%", + width: "90%", + onComplete: (function(_this) { + return function() { + var filename, getSvgXml; + root.create_lod_chart(); + filename = "lod_chart_" + js_data.this_trait; + getSvgXml = function() { + var svg; + svg = $("#topchart").find("svg")[0]; + return (new XMLSerializer).serializeToString(svg); + }; + $("#exportform > #export").click(function() { + var form, svg_xml; + svg_xml = getSvgXml(); + form = $("#exportform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }); + return $("#exportpdfform > #export_pdf").click(function() { + var form, svg_xml; + svg_xml = getSvgXml(); + form = $("#exportpdfform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }); + }; + })(this) + }); +}; - $("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) { - return function() { - if ($(".outlier").length && $(".outlier-alert").length < 1) { - return showalert(outlier_text, "alert-success outlier-alert"); - } - }; - })(this)); +outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results."; +showalert = function(message, alerttype) { + return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>'); +}; - composite_mapping_fields = function() { - return $(".composite_fields").toggle(); - }; +$('#suggestive').hide(); - mapping_method_fields = function() { - return $(".mapping_method_fields").toggle(); +$('input[name=display_all]').change((function(_this) { + return function() { + console.log("check"); + if ($('input[name=display_all]:checked').val() === "False") { + return $('#suggestive').show(); + } else { + return $('#suggestive').hide(); + } }; +})(this)); - $("#use_composite_choice").change(composite_mapping_fields); - - $("#mapping_method_choice").change(mapping_method_fields); +//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', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', + 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', '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', + 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples'] - $("#mapmodel_rqtl_geno").change(function() { - if ($(this).val() == "np"){ - $("#mapmethod_rqtl_geno").attr('disabled', 'disabled'); - $("#mapmethod_rqtl_geno").css('background-color', '#CCC'); - $("#missing_geno").attr('disabled', 'disabled'); - $("#missing_geno").css('background-color', '#CCC'); +$(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){ + var form_data, url; + url = "/loading"; + $('input[name=method]').val("rqtl_geno"); + $('input[name=selected_chr]').val($('#chr_rqtl_geno').val()); + $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val()); + $('input[name=genofile]').val($('#genofile_rqtl_geno').val()); + $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val()); + $('input[name=categorical_vars]').val(js_data.categorical_vars) + $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val()); + $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val()); + $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').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); } else { - $("#mapmethod_rqtl_geno").removeAttr('disabled'); - $("#mapmethod_rqtl_geno").css('background-color', '#FFF'); - $("#missing_geno").removeAttr('disabled'); - $("#missing_geno").css('background-color', '#FFF'); + return true } - }); + }; +})(this)); - $("#mapmethod_rqtl_geno").change(function() { - if ($(this).val() == "mr"){ - $("#missing_geno_div").css('display', 'block'); +$(".gemma_tab, #gemma_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){ + var form_data, url; + console.log("RUNNING GEMMA"); + url = "/loading"; + $('input[name=method]').val("gemma"); + $('input[name=selected_chr]').val($('#chr_gemma').val()); + $('input[name=num_perm]').val(0); + $('input[name=genofile]').val($('#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); } else { - $("#missing_geno_div").css('display', 'none'); + return true } - }); + }; +})(this)); - $("li.mapping_tab").click(function() { - if ($(this).hasClass("rqtl")){ - $(".rqtl_description").css("display", "block"); +$(".reaper_tab, #interval_mapping_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){ + var form_data, url; + console.log("In interval mapping"); + url = "/loading"; + $('input[name=method]').val("reaper"); + $('input[name=selected_chr]').val($('#chr_reaper').val()); + $('input[name=mapping_scale]').val($('#scale_reaper').val()); + $('input[name=genofile]').val($('#genofile_reaper').val()); + $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val()); + $('input[name=control_marker]').val($('input[name=control_reaper]').val()); + $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val()); + $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val()); + $('input[name=mapping_display_all]').val($('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); } else { - $(".rqtl_description").css("display", "none"); + return true } - }); + }; +})(this)); - toggle_enable_disable = function(elem) { - return $(elem).prop("disabled", !$(elem).prop("disabled")); +$("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) { + return function() { + if ($(".outlier").length && $(".outlier-alert").length < 1) { + return showalert(outlier_text, "alert-success outlier-alert"); + } }; +})(this)); - $("#choose_closet_control").change(function() { - return toggle_enable_disable("#control_locus"); - }); +composite_mapping_fields = function() { + return $(".composite_fields").toggle(); +}; - $("#display_all_lrs").change(function() { - return toggle_enable_disable("#suggestive_lrs"); - }); +mapping_method_fields = function() { + return $(".mapping_method_fields").toggle(); +}; - $('#genofile_rqtl_geno').change(function() { - geno_location = $(this).children("option:selected").val().split(":")[0] - $('#scale_rqtl_geno').empty() - the_scales = js_data.scales_in_geno[geno_location] - for (var i = 0; i < the_scales.length; i++){ - $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); - } - }); - $('#genofile_reaper').change(function() { - geno_location = $(this).children("option:selected").val().split(":")[0] - $('#scale_reaper').empty() - the_scales = js_data.scales_in_geno[geno_location] - for (var i = 0; i < the_scales.length; i++){ - $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); - } - }); +$("#use_composite_choice").change(composite_mapping_fields); + +$("#mapping_method_choice").change(mapping_method_fields); + +$("#mapmodel_rqtl_geno").change(function() { + if ($(this).val() == "np"){ + $("#mapmethod_rqtl_geno").attr('disabled', 'disabled'); + $("#mapmethod_rqtl_geno").css('background-color', '#CCC'); + $("#missing_geno").attr('disabled', 'disabled'); + $("#missing_geno").css('background-color', '#CCC'); + } else { + $("#mapmethod_rqtl_geno").removeAttr('disabled'); + $("#mapmethod_rqtl_geno").css('background-color', '#FFF'); + $("#missing_geno").removeAttr('disabled'); + $("#missing_geno").css('background-color', '#FFF'); + } +}); + +$("#mapmethod_rqtl_geno").change(function() { + if ($(this).val() == "mr"){ + $("#missing_geno_div").css('display', 'block'); + } else { + $("#missing_geno_div").css('display', 'none'); + } +}); + +$("li.mapping_tab").click(function() { + if ($(this).hasClass("rqtl")){ + $(".rqtl_description").css("display", "block"); + } else { + $(".rqtl_description").css("display", "none"); + } +}); + +toggle_enable_disable = function(elem) { + return $(elem).prop("disabled", !$(elem).prop("disabled")); +}; + +$("#choose_closet_control").change(function() { + return toggle_enable_disable("#control_locus"); +}); + +$("#display_all_lrs").change(function() { + return toggle_enable_disable("#suggestive_lrs"); +}); -}).call(this); +$('#genofile_rqtl_geno').change(function() { + geno_location = $(this).children("option:selected").val().split(":")[0] + $('#scale_rqtl_geno').empty() + the_scales = js_data.scales_in_geno[geno_location] + for (var i = 0; i < the_scales.length; i++){ + $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); + } +}); +$('#genofile_reaper').change(function() { + geno_location = $(this).children("option:selected").val().split(":")[0] + $('#scale_reaper').empty() + the_scales = js_data.scales_in_geno[geno_location] + for (var i = 0; i < the_scales.length; i++){ + $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); + } +}); diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index bc487a59..d1a97310 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -8,7 +8,7 @@ {% block content %} <!-- Start of body --> - <div class="container" style="min-width: 2050px;"> + <div class="container"> <h1> <span id="collection_name">{{ uc.name }}</span> <input type="text" name="new_collection_name" style="font-size: 20px; display: none; width: 500px;" class="form-control" placeholder="{{ uc.name }}"> @@ -85,7 +85,7 @@ <div style="margin-top: 10px; margin-bottom: 5px;"> <b>Show/Hide Columns:</b> </div> - <div> + <div style="min-width: 1500px;"> <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;"> <thead> <tr> @@ -97,7 +97,7 @@ <th data-export="Description">Description</th> <th data-export="Location">Location</th> <th data-export="Mean">Mean</th> - <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th> + <th data-export="Max LRS">High P <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th> <th data-export="Peak Location">Peak Location</th> <th data-export="Add. Eff.">Effect Size <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th> </tr> @@ -195,11 +195,11 @@ { 'type': "natural-minus-na", "width": 120 }, { "type": "natural" }, { "type": "natural" }, - { "type": "natural", "width": 130 }, - { "type": "natural", "width": 35 }, - { "type": "natural", "width": 35 }, - { "type": "natural", "width": 130 }, - { "type": "natural" } + { "type": "natural", "width": 125 }, + { "type": "natural", "width": 60 }, + { "type": "natural", "width": 60 }, + { "type": "natural", "width": 125 }, + { "type": "natural", "width": 85 } ], "order": [[1, "asc" ]], buttons: [ diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index e2e1aa46..2318bfb8 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -140,7 +140,6 @@ <b>Show/Hide Columns:</b> </div> {% endif %} - <!--<div id="table_container" style="min-width: {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}2000{% else %}380{% endif %}px;">--> <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}> <table class="table-hover table-striped cell-border" id='trait_table' style="float: left; width: {% if dataset.type == 'Geno' %}380px{% else %}100%{% endif %};"> <tbody> @@ -290,7 +289,6 @@ { 'title': "Description", 'type': "natural", - 'width': "500px", 'data': null, 'render': function(data, type, row, meta) { try { @@ -303,7 +301,7 @@ { 'title': "Location", 'type': "natural-minus-na", - 'width': "120px", + 'width': "125px", 'data': "location" }, { @@ -314,23 +312,23 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", + 'title': "High P<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", 'type': "natural-minus-na", 'data': "lrs_score", - 'width': "80px", + 'width': "60px", 'orderSequence': [ "desc", "asc"] }, { 'title': "Peak Location", 'type': "natural-minus-na", - 'width': "120px", + 'width': "125px", 'data': "lrs_location" }, { 'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", 'type': "natural-minus-na", 'data': "additive", - 'width': "120px", + 'width': "85px", 'orderSequence': [ "desc", "asc"] }{% elif dataset.type == 'Publish' %}, { diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 56df2049..5ed7a90b 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -37,7 +37,7 @@ <input type="hidden" name="covariates" value=""> <input type="hidden" name="transform" value=""> - <div class="container" style="min-width: 1450px;"> + <div class="container" style="min-width: 700px;"> <div class="panel-group" id="accordion"> <div class="panel panel-default"> <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true"> @@ -143,15 +143,18 @@ <script type="text/javascript" src="/static/new/javascript/plotly_probability_plot.js"></script> <script type="text/javascript" src="/static/new/javascript/compare_traits_scatterplot.js"></script> - <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script> - <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script> - <script type="text/javascript" src="/static/new/javascript/validation.js"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> + <script type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script> + + <script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script> + <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script> + <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script> + <script type="text/javascript" src="/static/new/javascript/validation.js"></script> + <script type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script> <script type="text/javascript" charset="utf-8"> @@ -208,162 +211,6 @@ } }); - //ZS: This variable is just created to get the column position of the first case attribute, since it's needed to set the row classes in createdRow for the DataTable - {% if sample_groups[0].attributes|length > 0 %} - {% if sample_groups[0].se_exists() %} - {% if has_num_cases %} - attribute_start_pos = 6 - {% else %} - attribute_start_pos = 5 - {% endif %} - {% else %} - {% if has_num_cases %} - attribute_start_pos = 4 - {% else %} - attribute_start_pos = 3 - {% endif %} - {% endif %} - {% endif %} - - var primary_table = $('#samples_primary').DataTable( { - 'initComplete': function(settings, json) { - $('.edit_sample_value').change(function() { - edit_data_change(); - }); - }, - 'createdRow': function ( row, data, index ) { - $(row).attr('id', "Primary_" + data.this_id) - $(row).addClass("value_se"); - if (data.outlier) { - $(row).addClass("outlier"); - } - $('td', row).eq(0).attr("align", "center"); - $('td', row).eq(0).attr("style", "padding: 2px 0px 0px 2px;"); - $('td', row).eq(1).addClass("column_name-Index") - $('td', row).eq(1).attr("align", "right"); - $('td', row).eq(1).attr("style", "padding: 2px 4px 0px 2px;"); - $('td', row).eq(2).addClass("column_name-Sample") - $('td', row).eq(3).addClass("column_name-Value") - $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); - {% if sample_groups[0].se_exists() %} - $('td', row).eq(4).attr("align", "center"); - $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;"); - $('td', row).eq(5).addClass("column_name-SE") - $('td', row).eq(5).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); - {% if has_num_cases %} - $('td', row).eq(6).addClass("column_name-num_cases") - $('td', row).eq(6).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); - {% endif %} {% else %} {% if has_num_cases %} - $('td', row).eq(4).addClass("column_name-num_cases") - $('td', row).eq(4).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); - {% endif %} {% endif %} - {% if sample_groups[0].attributes|length > 0 %} - {% for attribute in sample_groups[0].attributes|sort() %} - $('td', row).eq(attribute_start_pos + {{ loop.index }}).addClass("column_name-{{ sample_groups[0].attributes[attribute].name }}") - $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[0].attributes[attribute].alignment }}; padding-top: 2px; padding-bottom: 0px;") - {% endfor %} - {% endif %} - }, - 'data': js_data['sample_lists'][0], - 'columns': [ - { - 'data': null, - 'orderDataType': "dom-checkbox", - 'searchable' : false, - 'render': function(data, type, row, meta) { - return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="">' - } - }, - { - 'title': "ID", - 'type': "natural", - 'searchable' : false, - 'data': "this_id" - }, - { - 'title': "Sample", - 'type': "natural", - 'data': null, - 'render': function(data, type, row, meta) { - return '<span class="edit_sample_sample_name">' + data.name + '</span>' - } - }, - { - 'title': "<div style='text-align: right;'>Value</div>", - 'orderDataType': "dom-input", - 'type': "cust-txt", - 'data': null, - 'render': function(data, type, row, meta) { - if (data.value == null) { - return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>' - } else { - return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>' - } - } - }{% if sample_groups[0].se_exists() %}, - { - 'bSortable': false, - 'type': "natural", - 'data': null, - 'searchable' : false, - 'render': function(data, type, row, meta) { - return '±' - } - }, - { - 'title': "<div style='text-align: right;'>SE</div>", - 'orderDataType': "dom-input", - 'type': "cust-txt", - 'data': null, - 'render': function(data, type, row, meta) { - if (data.variance == null) { - return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>' - } else { - return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>' - } - } - }{% endif %}{% if has_num_cases %}, - { - 'title': "<div style='text-align: right;'>N</div>", - 'orderDataType': "dom-input", - 'type': "cust-txt", - 'data': null, - 'render': function(data, type, row, meta) { - if (data.num_cases == null || data.num_cases == undefined) { - return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>' - } else { - return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>' - } - } - }{% endif %}{% if sample_groups[0].attributes|length > 0 %}{% for attribute in sample_groups[0].attributes|sort() %}, - { - 'title': "<div style='text-align: {{ sample_groups[0].attributes[attribute].alignment }}'>{{ sample_groups[0].attributes[attribute].name }}</div>", - 'type': "natural", - 'data': null, - 'render': function(data, type, row, meta) { - if (data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}'] != null && data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}'] != undefined){ - return data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}'] - } else { - return "" - } - } - }{% endfor %}{% endif %} - ], - 'order': [[1, "asc"]], - 'sDom': "Ztr", - 'autoWidth': true, - 'deferRender': true, - 'paging': false, - 'orderClasses': true, - 'scrollY': "600px", - 'scrollCollapse': false, - 'processing': true, - 'language': { - 'loadingRecords': ' ', - 'processing': 'Loading...' - } - } ); - primary_table.on( 'order.dt search.dt draw.dt', function () { primary_table.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) { cell.innerHTML = i+1; @@ -375,145 +222,6 @@ } ); {% if sample_groups|length != 1 %} - var other_table = $('#samples_other').DataTable( { - 'initComplete': function(settings, json) { - $('.edit_sample_value').change(function() { - edit_data_change(); - }); - }, - 'createdRow': function ( row, data, index ) { - $(row).attr('id', "Other_" + data.this_id) - $(row).addClass("value_se"); - if (data.outlier) { - $(row).addClass("outlier"); - } - $('td', row).eq(0).attr("align", "center"); - $('td', row).eq(0).attr("style", "padding: 2px 0px 0px 2px;"); - $('td', row).eq(1).addClass("column_name-Index") - $('td', row).eq(1).attr("align", "right"); - $('td', row).eq(1).attr("style", "padding: 2px 4px 0px 2px;"); - $('td', row).eq(2).addClass("column_name-Sample") - $('td', row).eq(3).addClass("column_name-Value") - $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); - {% if sample_groups[1].se_exists() %} - $('td', row).eq(4).attr("align", "center"); - $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;"); - $('td', row).eq(5).addClass("column_name-SE") - $('td', row).eq(5).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); - {% if has_num_cases %} - $('td', row).eq(6).addClass("column_name-num_cases") - $('td', row).eq(6).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); - {% endif %} {% else %} {% if has_num_cases %} - $('td', row).eq(4).addClass("column_name-num_cases") - $('td', row).eq(4).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); - {% endif %} {% endif %} - {% if sample_groups[1].attributes|length > 0 %} - {% for attribute in sample_groups[1].attributes|sort() %} - $('td', row).eq(attribute_start_pos + {{ loop.index }}).addClass("column_name-{{ sample_groups[1].attributes[attribute].name }}") - $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[1].attributes[attribute].alignment }}; padding-top: 2px; padding-bottom: 0px;") - {% endfor %} - {% endif %} - }, - 'data': js_data['sample_lists'][1], - 'columns': [ - { - 'data': null, - 'orderDataType': "dom-checkbox", - 'searchable' : false, - 'render': function(data, type, row, meta) { - return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="">' - } - }, - { - 'title': "ID", - 'type': "natural", - 'data': "this_id", - 'searchable' : false - }, - { - 'title': "Sample", - 'type': "natural", - 'data': null, - 'render': function(data, type, row, meta) { - return '<span class="edit_sample_sample_name">' + data.name + '</span>' - } - }, - { - 'title': "<div style='text-align: right;'>Value</div>", - 'orderDataType': "dom-input", - 'type': "cust-txt", - 'data': null, - 'render': function(data, type, row, meta) { - if (data.value == null) { - return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>' - } else { - return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][1][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>' - } - } - }{% if sample_groups[1].se_exists() %}, - { - 'bSortable': false, - 'type': "natural", - 'data': null, - 'searchable' : false, - 'render': function(data, type, row, meta) { - return '±' - } - }, - { - 'title': "<div style='text-align: right;'>SE</div>", - 'orderDataType': "dom-input", - 'type': "cust-txt", - 'data': null, - 'render': function(data, type, row, meta) { - if (data.variance == null) { - return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>' - } else { - return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>' - } - } - }{% endif %}{% if has_num_cases %}, - { - 'title': "<div style='text-align: right;'>N</div>", - 'orderDataType': "dom-input", - 'type': "cust-txt", - 'data': null, - 'render': function(data, type, row, meta) { - if (data.num_cases == null) { - return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>' - } else { - return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>' - } - } - }{% endif %}{% if sample_groups[1].attributes|length > 0 %}{% for attribute in sample_groups[1].attributes|sort() %}, - { - 'title': "<div style='text-align: {{ sample_groups[1].attributes[attribute].alignment }}'>{{ sample_groups[1].attributes[attribute].name }}</div>", - 'type': "natural", - 'data': null, - 'render': function(data, type, row, meta) { - if (data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}'] != null && data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}'] != undefined){ - return data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}'] - } else { - return "" - } - } - }{% endfor %}{% endif %} - ], - 'order': [[1, "asc"]], - 'sDom': "Ztr", - 'autoWidth': true, - 'deferRender': true, - 'paging': false, - 'orderClasses': true, - 'scrollY': "600px", - 'scrollCollapse': false, - 'processing': true, - 'language': { - 'loadingRecords': ' ', - 'processing': 'Loading...' - } - } ); - $('#other_searchbox').on( 'keyup', function () { other_table.search($(this).val()).draw(); } ); diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index 1378b91b..9420c9c6 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -1,5 +1,5 @@ <div> - <div class="col-xs-7"> + <div class="col-xs-6" style="min-width: 800px;"> <div style="padding: 20px" class="form-horizontal"> <div class="form-group"> @@ -39,7 +39,7 @@ <div class="form-group"> <label for="corr_return_results" class="col-xs-2 control-label">Return</label> - <div class="col-xs-3 controls"> + <div class="col-xs-4 controls"> <select name="corr_return_results" class="form-control"> {% for return_result in corr_tools.return_results_menu %} <option value="{{ return_result }}" @@ -55,7 +55,7 @@ <div class="form-group"> <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label> - <div class="col-xs-3 controls"> + <div class="col-xs-4 controls"> <select name="corr_samples_group" class="form-control"> {% for group, pretty_group in sample_group_types.items() %} <option value="{{ group }}">{{ pretty_group }}</option> @@ -66,7 +66,7 @@ <div id="corr_sample_method" class="form-group"> <label for="corr_sample_method" class="col-xs-2 control-label">Type</label> - <div class="col-xs-3 controls"> + <div class="col-xs-4 controls"> <select name="corr_sample_method" class="form-control"> <option value="pearson">Pearson</option> <option value="spearman">Spearman Rank</option> @@ -77,7 +77,7 @@ {% if dataset.type != "Publish" %} <div class="form-group"> <label class="col-xs-2 control-label">Min Expr</label> - <div class="col-xs-3 controls"> + <div class="col-xs-4 controls"> <input name="min_expr" value="" type="text" class="form-control" style="width: 70px;"> </div> </div> @@ -114,7 +114,7 @@ </div> </div> </div> - <div class="col-xs-5"> + <div> <span id="sample_r_desc" class="correlation_desc fs12"> The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a> is computed diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 27040045..94388b2f 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -397,8 +397,8 @@ </div> </div> </div> - <div class="col-xs-7"> - <dl style="width: 500px;"> + <div> + <dl> {% for mapping_method in dataset.group.mapping_names %} {% if mapping_method == "GEMMA" %} <dt style="padding-top: 20px;">GEMMA</dt> diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index b4118b04..9fb560a0 100644 --- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -1,83 +1,78 @@ <div> - <div class="form-horizontal"> - <p>Edit or delete values in the Trait Data boxes, and use the - <strong>Reset</strong> option as - needed. - </p> + <div class="form-horizontal"> + <p>Edit or delete values in the Trait Data boxes, and use the + <strong>Reset</strong> option as + needed. + </p> - <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;"> - <label for="remove_samples_field">Block samples by index:</label> - <input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12"> - <select id="block_group" size="1"> - <option value="primary"> - {{ sample_group_types['samples_primary'] }} - </option> - <option value="other"> - {{ sample_group_types['samples_other'] }} - </option> - </select> - <input type="button" id="block_by_index" class="btn btn-danger" value="Block"> - </div> - <div id="remove_samples_invalid" class="alert alert-error" style="display:none;"> - Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong> - </div> - {% if sample_groups[0].attributes %} - <div class="input-append" style="margin-top:10px; margin-bottom:10px;"> - <label for="exclude_menu">Block samples by group:</label> - <select id="exclude_menu" size=1> - {% for attribute in sample_groups[0].attributes %} - <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}"> - {{ sample_groups[0].attributes[attribute].name }}</option> - {% endfor %} - </select> - <select id="attribute_values" size=1> - </select> - <input type="button" id="exclude_group" class="btn" value="Block"> - </div> - {% endif %} - <div> - <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value"> - <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers"> - <input type="button" class="btn btn-success reset" value="Reset"> - <span class="input-append"> - <input type="button" class="btn btn-default export" value="Export"> - <select class="select optional span2 export_format"> - <option value="excel">Excel</option> - <option value="csv">CSV</option> - </select> - </span> - <br> - <div style="margin-top:10px;"> - <input type="button" id="normalize" class="btn btn-success" value="Normalize"> - <select id="norm_method" class="select optional span2"> - {% if negative_vals_exist == "false" %} - <option value="log2">Log2</option> - <option value="log10">Log10</option> - {% endif %} - <option value="zscore">Z-score</option> - <option value="qnorm">Quantile</option> - <option value="sqrt">Square Root</option> - <option value="invert">Invert +/-</option> + <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;"> + <label for="remove_samples_field">Block samples by index:</label> + <input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12"> + <select id="block_group" size="1"> + <option value="primary"> + {{ sample_group_types['samples_primary'] }} + </option> + <option value="other"> + {{ sample_group_types['samples_other'] }} + </option> + </select> + <input type="button" id="block_by_index" class="btn btn-danger" value="Block"> + </div> + <div id="remove_samples_invalid" class="alert alert-error" style="display:none;"> + Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong> + </div> + {% if sample_groups[0].attributes %} + <div class="input-append" style="margin-top:10px; margin-bottom:10px;"> + <label for="exclude_menu">Block samples by group:</label> + <select id="exclude_menu" size=1> + {% for attribute in sample_groups[0].attributes %} + <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}"> + {{ sample_groups[0].attributes[attribute].name }}</option> + {% endfor %} + </select> + <select id="attribute_values" size=1> + </select> + <input type="button" id="exclude_group" class="btn" value="Block"> + </div> + {% endif %} + <div> + <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value"> + <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers"> + <input type="button" class="btn btn-success reset" value="Reset"> + <span class="input-append"> + <input type="button" class="btn btn-default export" value="Export"> + <select class="select optional span2 export_format"> + <option value="excel">Excel</option> + <option value="csv">CSV</option> </select> - </div> - <!-- - {% if sample_groups[0].sample_qnorm is not none %} - <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize"> + </span> + <br> + <div style="margin-top:10px;"> + <input type="button" id="normalize" class="btn btn-success" value="Normalize"> + <select id="norm_method" class="select optional span2"> + {% if negative_vals_exist == "false" %} + <option value="log2">Log2</option> + <option value="log10">Log10</option> + <option value="sqrt">Square Root</option> {% endif %} - --> + <option value="zscore">Z-score</option> + <option value="qnorm">Quantile</option> + <option value="invert">Invert +/-</option> + </select> </div> - <br> + </div> + <br> - <div> - <p>Outliers highlighted in - <strong style="background-color:orange;">orange</strong> - can be hidden using - the <strong>Hide Outliers</strong> button. - </p> + <div> + <p>Outliers highlighted in + <strong style="background-color:orange;">orange</strong> + can be hidden using + the <strong>Hide Outliers</strong> button. + </p> - <p>Samples with no value (x) can be hidden by clicking - <strong>Hide No Value</strong> button. - </p> - </div> - </div> + <p>Samples with no value (x) can be hidden by clicking + <strong>Hide No Value</strong> button. + </p> + </div> + </div> </div>
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