diff options
| -rw-r--r-- | misc/gn_installation_notes.txt | 6 | ||||
| -rw-r--r-- | misc/notes.txt | 3 | ||||
| -rwxr-xr-x | wqflask/base/data_set.py | 1 | ||||
| -rwxr-xr-x | wqflask/base/trait.py | 6 | ||||
| -rw-r--r-- | wqflask/other_config/nginx_conf/penguin.conf | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 15 | ||||
| -rwxr-xr-x[-rw-r--r--] | wqflask/wqflask/interval_mapping/interval_mapping.py | 70 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/SampleList.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/css/bar_chart.css | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.coffee | 264 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 271 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_page.html | 119 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/quick_search.html | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_statistics_new.html | 29 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 44 |
17 files changed, 755 insertions, 104 deletions
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt index a73e7d4f..584080f7 100644 --- a/misc/gn_installation_notes.txt +++ b/misc/gn_installation_notes.txt @@ -304,6 +304,12 @@ sudo apt-get install colordiff ========================================== +Install NTP (network time protocol) + +sudo apt-get install ntp + +========================================== + To get server running: !If having seemingly inexplicable problems with imports, make sure I've started the environment! diff --git a/misc/notes.txt b/misc/notes.txt index 91a0e67c..f6a2bb33 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -90,6 +90,9 @@ Reload web server: Run server: python runserver.py +Run sendmail.py +python send_mail.py + =========================================== UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index f25e7974..cd8c1ac1 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -224,6 +224,7 @@ class DatasetGroup(object): """ def __init__(self, dataset): """This sets self.group and self.group_id""" + print("dataset name:", dataset.name) self.name, self.id = g.db.execute(dataset.query_for_group).fetchone() if self.name == 'BXD300': self.name = "BXD" diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index aea1f9a9..731f99eb 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -387,6 +387,7 @@ class GeneralTrait(object): #trait_qtl = self.cursor.fetchone() if trait_qtl: self.locus, self.lrs, self.pvalue, self.mean = trait_qtl + print("self.locus:", self.locus) if self.locus: query = """ select Geno.Chr, Geno.Mb from Geno, Species @@ -395,8 +396,9 @@ class GeneralTrait(object): Geno.SpeciesId = Species.Id """.format(self.dataset.group.species, self.locus) result = g.db.execute(query).fetchone() - self.locus_chr = result[0] - self.locus_mb = result[1] + if result: + self.locus_chr = result[0] + self.locus_mb = result[1] else: self.locus = self.locus_chr = self.locus_mb = self.lrs = self.pvalue = self.mean = "" diff --git a/wqflask/other_config/nginx_conf/penguin.conf b/wqflask/other_config/nginx_conf/penguin.conf index 822556d3..5c380da8 100644 --- a/wqflask/other_config/nginx_conf/penguin.conf +++ b/wqflask/other_config/nginx_conf/penguin.conf @@ -2,7 +2,7 @@ server { # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/ listen 80; - server_name penguin.uthsc.edu; + server_name gn2python.genenetwork.org; access_log /var/log/nginx/access.log; error_log /var/log/nginx/error.log; diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 8f23165c..0b66bc61 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -102,6 +102,7 @@ class CorrelationResults(object): self.sample_data = {} self.corr_type = start_vars['corr_type'] self.corr_method = start_vars['corr_sample_method'] + self.get_formatted_corr_type() self.return_number = 50 #The two if statements below append samples to the sample list based upon whether the user @@ -239,6 +240,20 @@ class CorrelationResults(object): ############################################################################################################################################ + def get_formatted_corr_type(self): + self.formatted_corr_type = "" + if self.corr_type == "lit": + self.formatted_corr_type += "Literature Correlation " + elif self.corr_type == "tissue": + self.formatted_corr_type += "Tissue Correlation " + elif self.corr_type == "sample": + self.formatted_corr_type += "Genetic Correlation " + + if self.corr_method == "pearson": + self.formatted_corr_type += "(Pearson's r)" + elif self.corr_method == "spearman": + self.formatted_corr_type += "(Spearman's rho)" + def do_tissue_correlation_for_trait_list(self, tissue_dataset_id=1): """Given a list of correlation results (self.correlation_results), gets the tissue correlation value for each""" diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py index 5d660224..aca99cbe 100644..100755 --- a/wqflask/wqflask/interval_mapping/interval_mapping.py +++ b/wqflask/wqflask/interval_mapping/interval_mapping.py @@ -89,26 +89,56 @@ class IntervalMapping(object): samples, values, variances = self.trait.export_informative() if self.control_locus: if self.weighted_regression: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values, variance = variances, control = self.control_locus) else: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values, control = self.control_locus) else: if self.weighted_regression: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values, variance = variances) else: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values) - pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) + #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) + + #if self.dataset.group.species == "human": + # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) + #else: + genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] + + no_val_samples = self.identify_empty_samples() + trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) + + genotype_matrix = np.array(trimmed_genotype_data).T + + #t_stats, p_values = lmm.run( + # pheno_vector, + # genotype_matrix, + # restricted_max_likelihood=True, + # refit=False, + # temp_data=tempdata + #) + + #self.dataset.group.markers.add_pvalues(p_values) + + #self.qtl_results = self.dataset.group.markers.markers + def gen_qtl_results_2(self, tempdata): + """Generates qtl results for plotting interval map""" + + self.dataset.group.get_markers() + self.dataset.read_genotype_file() + + pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) + #if self.dataset.group.species == "human": # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) #else: @@ -131,36 +161,6 @@ class IntervalMapping(object): self.qtl_results = self.dataset.group.markers.markers - #def gen_qtl_results_2(self, tempdata): - # """Generates qtl results for plotting interval map""" - # - # self.dataset.group.get_markers() - # self.dataset.read_genotype_file() - # - # pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) - # - # #if self.dataset.group.species == "human": - # # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) - # #else: - # genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] - # - # no_val_samples = self.identify_empty_samples() - # trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) - # - # genotype_matrix = np.array(trimmed_genotype_data).T - # - # t_stats, p_values = lmm.run( - # pheno_vector, - # genotype_matrix, - # restricted_max_likelihood=True, - # refit=False, - # temp_data=tempdata - # ) - # - # self.dataset.group.markers.add_pvalues(p_values) - # - # self.qtl_results = self.dataset.group.markers.markers - def identify_empty_samples(self): no_val_samples = [] diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 1130fb60..9cd7d895 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -138,7 +138,7 @@ class SampleList(object): StrainId = %s AND CaseAttributeId = %s group by CaseAttributeXRef.CaseAttributeId""", ( - self.this_trait.db.id, sample_id, str(attribute))) + self.this_trait.dataset.id, sample_id, str(attribute))) attribute_value = result.fetchone().Value #Trait-specific attributes, if any diff --git a/wqflask/wqflask/static/new/css/bar_chart.css b/wqflask/wqflask/static/new/css/bar_chart.css new file mode 100644 index 00000000..ba14fe4e --- /dev/null +++ b/wqflask/wqflask/static/new/css/bar_chart.css @@ -0,0 +1,14 @@ +.axis path, +.axis line { + fill: none; + stroke: #000; + shape-rendering: crispEdges; +} + +.bar { + fill: steelblue; +} + +.x.axis path { + display: none; +} \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index 0f16ac68..66110469 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -56,16 +56,271 @@ Stat_Table_Rows = [ url: "/glossary.html#Interquartile" digits: 2 } - ] $ -> + class Histogram + constructor: (@sample_list, @sample_group) -> + @get_samples() + console.log("sample names:", @sample_names) + + #Used to calculate the bottom margin so sample names aren't cut off + longest_sample_name = d3.max(sample.length for sample in @sample_names) + + @margin = {top: 20, right: 20, bottom: longest_sample_name * 7, left: 40} + @plot_width = @sample_vals.length * 15 - @margin.left - @margin.right + @plot_height = 500 - @margin.top - @margin.bottom + + @x_buffer = @plot_width/20 + @y_buffer = @plot_height/20 + + @y_min = d3.min(@sample_vals) + @y_max = d3.max(@sample_vals) * 1.1 + + @svg = @create_svg() + + @plot_height -= @y_buffer + @create_scales() + @create_graph() + + d3.select("#color_attribute").on("change", => + attribute = $("#color_attribute").val() + if $("#update_bar_chart").html() == 'Sort By Name' + @svg.selectAll(".bar") + .data(@sorted_samples()) + .transition() + .duration(1000) + .style("fill", (d) => + if attribute == "None" + return "steelblue" + else + return @attr_color_dict[attribute][d[2][attribute]] + ) + .select("title") + .text((d) => + return d[1] + ) + else + @svg.selectAll(".bar") + .data(@samples) + .transition() + .duration(1000) + .style("fill", (d) => + if attribute == "None" + return "steelblue" + else + return @attr_color_dict[attribute][d[2][attribute]] + ) + ) + + + d3.select("#update_bar_chart").on("click", => + if @attributes.length > 0 + attribute = $("#color_attribute").val() + if $("#update_bar_chart").html() == 'Sort By Value' + $("#update_bar_chart").html('Sort By Name') + sortItems = (a, b) -> + return a[1] - b[1] + + @svg.selectAll(".bar") + .data(@sorted_samples()) + .transition() + .duration(1000) + .attr("y", (d) => + return @y_scale(d[1]) + ) + .attr("height", (d) => + return @plot_height - @y_scale(d[1]) + ) + .style("fill", (d) => + if @attributes.length > 0 + return @attr_color_dict[attribute][d[2][attribute]] + else + return "steelblue" + ) + .select("title") + .text((d) => + return d[1] + ) + sorted_sample_names = (sample[0] for sample in @sorted_samples()) + x_scale = d3.scale.ordinal() + .domain(sorted_sample_names) + .rangeBands([0, @plot_width], .1) + $('.x.axis').remove() + @add_x_axis(x_scale) + else + $("#update_bar_chart").html('Sort By Value') + @svg.selectAll(".bar") + .data(@samples) + .transition() + .duration(1000) + .attr("y", (d) => + return @y_scale(d[1]) + ) + .attr("height", (d) => + return @plot_height - @y_scale(d[1]) + ) + .style("fill", (d) => + if @attributes.length > 0 + return @attr_color_dict[attribute][d[2][attribute]] + else + return "steelblue" + ) + .select("title") + .text((d) => + return d[1] + ) + x_scale = d3.scale.ordinal() + .domain(@sample_names) + .rangeBands([0, @plot_width], .1) + $('.x.axis').remove() + @add_x_axis(x_scale) + ) + + get_attr_color_dict: () -> + color = d3.scale.category20() + @attr_color_dict = {} + for own key, attribute_info of js_data.attribute_names + this_color_dict = {} + for value, i in attribute_info.distinct_values + this_color_dict[value] = color(i) + @attr_color_dict[attribute_info.name] = this_color_dict + + + + + get_samples: () -> + @sample_names = (sample.name for sample in @sample_list when sample.value != null) + @sample_vals = (sample.value for sample in @sample_list when sample.value != null) + @attributes = (key for key of @sample_list[0]["extra_attributes"]) + console.log("attributes:", @attributes) + @sample_attr_vals = [] + if @attributes.length > 0 + for sample in @sample_list + attr_vals = {} + for attribute in @attributes + attr_vals[attribute] = sample["extra_attributes"][attribute] + @sample_attr_vals.push(attr_vals) + @samples = _.zip(@sample_names, @sample_vals, @sample_attr_vals) + @get_attr_color_dict() + console.log("samples:", @samples) + + create_svg: () -> + svg = d3.select("#bar_chart") + .append("svg") + .attr("class", "bar_chart") + .attr("width", @plot_width + @margin.left + @margin.right) + .attr("height", @plot_height + @margin.top + @margin.bottom) + .append("g") + .attr("transform", "translate(" + @margin.left + "," + @margin.top + ")") + + return svg + + create_scales: () -> + @x_scale = d3.scale.ordinal() + .domain(@sample_names) + .rangeBands([0, @plot_width], .1) + + @y_scale = d3.scale.linear() + .domain([@y_min * 0.75, @y_max]) + .range([@plot_height, @y_buffer]) + + create_graph: () -> + + #@add_border() + @add_x_axis(@x_scale) + @add_y_axis() + + @add_bars() + + add_x_axis: (scale) -> + xAxis = d3.svg.axis() + .scale(scale) + .orient("bottom"); + + @svg.append("g") + .attr("class", "x axis") + .attr("transform", "translate(0," + @plot_height + ")") + .call(xAxis) + .selectAll("text") + .style("text-anchor", "end") + .style("font-size", "12px") + .attr("dx", "-.8em") + .attr("dy", "-.3em") + .attr("transform", (d) => + return "rotate(-90)" + ) + + add_y_axis: () -> + yAxis = d3.svg.axis() + .scale(@y_scale) + .orient("left") + .ticks(5) + + @svg.append("g") + .attr("class", "y axis") + .call(yAxis) + .append("text") + .attr("transform", "rotate(-90)") + .attr("y", 6) + .attr("dy", ".71em") + .style("text-anchor", "end") + + add_bars: () -> + @svg.selectAll(".bar") + .data(@samples) + .enter().append("rect") + .style("fill", "steelblue") + .attr("class", "bar") + .attr("x", (d) => + return @x_scale(d[0]) + ) + .attr("width", @x_scale.rangeBand()) + .attr("y", (d) => + return @y_scale(d[1]) + ) + .attr("height", (d) => + return @plot_height - @y_scale(d[1]) + ) + .append("svg:title") + .text((d) => + return d[1] + ) + + sorted_samples: () -> + #if @sample_attr_vals.length > 0 + sample_list = _.zip(@sample_names, @sample_vals, @sample_attr_vals) + #else + # sample_list = _.zip(@sample_names, @sample_vals) + sorted = _.sortBy(sample_list, (sample) => + return sample[1] + ) + console.log("sorted:", sorted) + return sorted + + sample_lists = js_data.sample_lists + sample_group_types = js_data.sample_group_types + + new Histogram(sample_lists[0]) + + $('.stats_samples_group').change -> + $('#bar_chart').remove() + $('#bar_chart_container').append('<div id="bar_chart"></div>') + group = $(this).val() + console.log("group:", group) + if group == "samples_primary" + new Histogram(sample_lists[0]) + else if group == "samples_other" + new Histogram(sample_lists[1]) + else if group == "samples_all" + all_samples = sample_lists[0].concat sample_lists[1] + new Histogram(all_samples) + + hide_tabs = (start) -> for x in [start..10] $("#stats_tabs" + x).hide() - #hide_tabs(1) - # Changes stats table between all, bxd only and non-bxd, etc. stats_mdp_change = -> selected = $(this).val() @@ -81,7 +336,6 @@ $ -> current_value = parseFloat($(in_box)).toFixed(decimal_places) - console.log("urgh:", category, value_type) the_value = sample_sets[category][value_type]() console.log("After running sample_sets, the_value is:", the_value) if decimal_places > 0 @@ -121,7 +375,6 @@ $ -> tables = ['samples_primary', 'samples_other'] for table in tables rows = $("#" + table).find('tr') - console.log("[fuji3] rows:", rows) for row in rows name = $(row).find('.edit_sample_sample_name').html() name = $.trim(name) @@ -180,7 +433,6 @@ $ -> $("#stats_table").append(table) - process_id = (values...) -> ### Make an id or a class valid javascript by, for example, eliminating spaces ### processed = "" diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index f554267f..4e7fe8f8 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -56,7 +56,274 @@ ]; $(function() { - var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, show_hide_outliers, stats_mdp_change, update_stat_values; + var Histogram, block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values; + Histogram = (function() { + + function Histogram(sample_list, sample_group) { + var longest_sample_name, sample, + _this = this; + this.sample_list = sample_list; + this.sample_group = sample_group; + this.get_samples(); + console.log("sample names:", this.sample_names); + longest_sample_name = d3.max((function() { + var _i, _len, _ref, _results; + _ref = this.sample_names; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + sample = _ref[_i]; + _results.push(sample.length); + } + return _results; + }).call(this)); + this.margin = { + top: 20, + right: 20, + bottom: longest_sample_name * 7, + left: 40 + }; + this.plot_width = this.sample_vals.length * 15 - this.margin.left - this.margin.right; + this.plot_height = 500 - this.margin.top - this.margin.bottom; + this.x_buffer = this.plot_width / 20; + this.y_buffer = this.plot_height / 20; + this.y_min = d3.min(this.sample_vals); + this.y_max = d3.max(this.sample_vals) * 1.1; + this.svg = this.create_svg(); + this.plot_height -= this.y_buffer; + this.create_scales(); + this.create_graph(); + d3.select("#color_attribute").on("change", function() { + var attribute; + attribute = $("#color_attribute").val(); + if ($("#update_bar_chart").html() === 'Sort By Name') { + return _this.svg.selectAll(".bar").data(_this.sorted_samples()).transition().duration(1000).style("fill", function(d) { + if (attribute === "None") { + return "steelblue"; + } else { + return _this.attr_color_dict[attribute][d[2][attribute]]; + } + }).select("title").text(function(d) { + return d[1]; + }); + } else { + return _this.svg.selectAll(".bar").data(_this.samples).transition().duration(1000).style("fill", function(d) { + if (attribute === "None") { + return "steelblue"; + } else { + return _this.attr_color_dict[attribute][d[2][attribute]]; + } + }); + } + }); + d3.select("#update_bar_chart").on("click", function() { + var attribute, sortItems, sorted_sample_names, x_scale; + if (_this.attributes.length > 0) { + attribute = $("#color_attribute").val(); + } + if ($("#update_bar_chart").html() === 'Sort By Value') { + $("#update_bar_chart").html('Sort By Name'); + sortItems = function(a, b) { + return a[1] - b[1]; + }; + _this.svg.selectAll(".bar").data(_this.sorted_samples()).transition().duration(1000).attr("y", function(d) { + return _this.y_scale(d[1]); + }).attr("height", function(d) { + return _this.plot_height - _this.y_scale(d[1]); + }).style("fill", function(d) { + if (_this.attributes.length > 0) { + return _this.attr_color_dict[attribute][d[2][attribute]]; + } else { + return "steelblue"; + } + }).select("title").text(function(d) { + return d[1]; + }); + sorted_sample_names = (function() { + var _i, _len, _ref, _results; + _ref = this.sorted_samples(); + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + sample = _ref[_i]; + _results.push(sample[0]); + } + return _results; + }).call(_this); + x_scale = d3.scale.ordinal().domain(sorted_sample_names).rangeBands([0, _this.plot_width], .1); + $('.x.axis').remove(); + return _this.add_x_axis(x_scale); + } else { + $("#update_bar_chart").html('Sort By Value'); + _this.svg.selectAll(".bar").data(_this.samples).transition().duration(1000).attr("y", function(d) { + return _this.y_scale(d[1]); + }).attr("height", function(d) { + return _this.plot_height - _this.y_scale(d[1]); + }).style("fill", function(d) { + if (_this.attributes.length > 0) { + return _this.attr_color_dict[attribute][d[2][attribute]]; + } else { + return "steelblue"; + } + }).select("title").text(function(d) { + return d[1]; + }); + x_scale = d3.scale.ordinal().domain(_this.sample_names).rangeBands([0, _this.plot_width], .1); + $('.x.axis').remove(); + return _this.add_x_axis(x_scale); + } + }); + } + + Histogram.prototype.get_attr_color_dict = function() { + var attribute_info, color, i, key, this_color_dict, value, _i, _len, _ref, _ref1, _results; + color = d3.scale.category20(); + this.attr_color_dict = {}; + _ref = js_data.attribute_names; + _results = []; + for (key in _ref) { + if (!__hasProp.call(_ref, key)) continue; + attribute_info = _ref[key]; + this_color_dict = {}; + _ref1 = attribute_info.distinct_values; + for (i = _i = 0, _len = _ref1.length; _i < _len; i = ++_i) { + value = _ref1[i]; + this_color_dict[value] = color(i); + } + _results.push(this.attr_color_dict[attribute_info.name] = this_color_dict); + } + return _results; + }; + + Histogram.prototype.get_samples = function() { + var attr_vals, attribute, key, sample, _i, _j, _len, _len1, _ref, _ref1; + this.sample_names = (function() { + var _i, _len, _ref, _results; + _ref = this.sample_list; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + sample = _ref[_i]; + if (sample.value !== null) { + _results.push(sample.name); + } + } + return _results; + }).call(this); + this.sample_vals = (function() { + var _i, _len, _ref, _results; + _ref = this.sample_list; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + sample = _ref[_i]; + if (sample.value !== null) { + _results.push(sample.value); + } + } + return _results; + }).call(this); + this.attributes = (function() { + var _results; + _results = []; + for (key in this.sample_list[0]["extra_attributes"]) { + _results.push(key); + } + return _results; + }).call(this); + console.log("attributes:", this.attributes); + this.sample_attr_vals = []; + if (this.attributes.length > 0) { + _ref = this.sample_list; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + sample = _ref[_i]; + attr_vals = {}; + _ref1 = this.attributes; + for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) { + attribute = _ref1[_j]; + attr_vals[attribute] = sample["extra_attributes"][attribute]; + } + this.sample_attr_vals.push(attr_vals); + } + } + this.samples = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals); + this.get_attr_color_dict(); + return console.log("samples:", this.samples); + }; + + Histogram.prototype.create_svg = function() { + var svg; + svg = d3.select("#bar_chart").append("svg").attr("class", "bar_chart").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")"); + return svg; + }; + + Histogram.prototype.create_scales = function() { + this.x_scale = d3.scale.ordinal().domain(this.sample_names).rangeBands([0, this.plot_width], .1); + return this.y_scale = d3.scale.linear().domain([this.y_min * 0.75, this.y_max]).range([this.plot_height, this.y_buffer]); + }; + + Histogram.prototype.create_graph = function() { + this.add_x_axis(this.x_scale); + this.add_y_axis(); + return this.add_bars(); + }; + + Histogram.prototype.add_x_axis = function(scale) { + var xAxis, + _this = this; + xAxis = d3.svg.axis().scale(scale).orient("bottom"); + return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(xAxis).selectAll("text").style("text-anchor", "end").style("font-size", "12px").attr("dx", "-.8em").attr("dy", "-.3em").attr("transform", function(d) { + return "rotate(-90)"; + }); + }; + + Histogram.prototype.add_y_axis = function() { + var yAxis; + yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); + return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end"); + }; + + Histogram.prototype.add_bars = function() { + var _this = this; + return this.svg.selectAll(".bar").data(this.samples).enter().append("rect").style("fill", "steelblue").attr("class", "bar").attr("x", function(d) { + return _this.x_scale(d[0]); + }).attr("width", this.x_scale.rangeBand()).attr("y", function(d) { + return _this.y_scale(d[1]); + }).attr("height", function(d) { + return _this.plot_height - _this.y_scale(d[1]); + }).append("svg:title").text(function(d) { + return d[1]; + }); + }; + + Histogram.prototype.sorted_samples = function() { + var sample_list, sorted, + _this = this; + sample_list = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals); + sorted = _.sortBy(sample_list, function(sample) { + return sample[1]; + }); + console.log("sorted:", sorted); + return sorted; + }; + + return Histogram; + + })(); + sample_lists = js_data.sample_lists; + sample_group_types = js_data.sample_group_types; + new Histogram(sample_lists[0]); + $('.stats_samples_group').change(function() { + var all_samples, group; + $('#bar_chart').remove(); + $('#bar_chart_container').append('<div id="bar_chart"></div>'); + group = $(this).val(); + console.log("group:", group); + if (group === "samples_primary") { + return new Histogram(sample_lists[0]); + } else if (group === "samples_other") { + return new Histogram(sample_lists[1]); + } else if (group === "samples_all") { + all_samples = sample_lists[0].concat(sample_lists[1]); + return new Histogram(all_samples); + } + }); hide_tabs = function(start) { var x, _i, _results; _results = []; @@ -77,7 +344,6 @@ console.log("the_id:", id); in_box = $(id).html; current_value = parseFloat($(in_box)).toFixed(decimal_places); - console.log("urgh:", category, value_type); the_value = sample_sets[category][value_type](); console.log("After running sample_sets, the_value is:", the_value); if (decimal_places > 0) { @@ -127,7 +393,6 @@ for (_i = 0, _len = tables.length; _i < _len; _i++) { table = tables[_i]; rows = $("#" + table).find('tr'); - console.log("[fuji3] rows:", rows); for (_j = 0, _len1 = rows.length; _j < _len1; _j++) { row = rows[_j]; name = $(row).find('.edit_sample_sample_name').html(); diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 7e149506..d675b801 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -9,55 +9,76 @@ {{ header("Correlation", 'Trait: {} Dataset: {}'.format(this_trait.name, dataset.name)) }} - <table id="corr_results" class="table table-hover table-striped table-bordered"> - <thead> - <tr> - <th>Trait</th> - <th>Symbol</th> - <th>Alias</th> - <th>Description</th> - <th>Location</th> - <th>Mean Expr</th> - <th>Max LRS</th> - <th>Max LRS Location</th> - {% if corr_method == 'pearson' %} - <th>Sample r</th> - <th>N Cases</th> - <th>Sample p(r)</th> - <th>Lit Corr</th> - <th>Tissue r</th> - <th>Tissue p(r)</th> - {% else %} - <th>Sample rho</th> - <th>Sample p(rho)</th> - <th>Lit Corr</th> - <th>Tissue rho</th> - <th>Tissue p(rho)</th> - {% endif %} + <div class="container"> + <div class="page-header"> + <h1>Correlation Table</h1> + </div> + + <p>Values of record {{ this_trait.name }} in the <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a> + dataset were compared to all records in the <a href="/dbdoc/{{target_dataset.fullname}}">{{ target_dataset.fullname }}</a> + dataset. The top {{ return_number }} correlations ranked by the {{ formatted_corr_type }} are displayed. + You can resort this list by clicking the headers. Select the Record ID to open the trait data + and analysis page. + </p> + + <div> + <table id="corr_results" class="table table-hover table-striped table-bordered"> + <thead> + <tr> + <th>Trait</th> + <th>Symbol</th> + <th>Description</th> + <th>Location</th> + <th>Mean Expr</th> + <th>Max LRS</th> + <th>Max LRS Location</th> + {% if corr_method == 'pearson' %} + <th>Sample r</th> + <th>N Cases</th> + <th>Sample p(r)</th> + <th>Lit Corr</th> + <th>Tissue r</th> + <th>Tissue p(r)</th> + {% else %} + <th>Sample rho</th> + <th>N Cases</th> + <th>Sample p(rho)</th> + <th>Lit Corr</th> + <th>Tissue rho</th> + <th>Tissue p(rho)</th> + {% endif %} + </tr> + </thead> + <tbody> + {% for trait in correlation_results %} + <tr> + <td><a href="/show_trait?trait_id={{trait.name}}&dataset={{trait.dataset.name}}">{{ trait.name }}</a></td> + <td>{{ trait.symbol }}</td> + <td>{{ trait.description }} <br><br> <b>Aliases</b>: {{ trait.alias }}</td> + <td>Chr{{ trait.chr }}: {{'%0.3f'|format(trait.mb) }}</td> + <td>{{'%0.3f'|format(trait.mean)}}</td> + <td>{{'%0.3f'|format(trait.lrs)}}</td> + <td>Chr{{ trait.locus_chr }}: {{'%0.3f'|format(trait.locus_mb) }}</td> + <td>{{'%0.3f'|format(trait.sample_r)}}</td> + <td>{{ trait.num_overlap }}</td> + <td>{{'%0.3e'|format(trait.sample_p)}}</td> + <td>{{'%0.3f'|format(trait.lit_corr)}}</td> + <td>{{'%0.3f'|format(trait.tissue_corr)}}</td> + <td>{{'%0.3e'|format(trait.tissue_pvalue)}}</td> + </tr> + {% endfor %} + </tbody> + </table> - </tr> - </thead> - <tbody> - {% for trait in correlation_results %} - <tr> - <td><a href="/show_trait?trait_id={{trait.name}}&dataset={{trait.dataset.name}}">{{ trait.name }}</a></td> - <td>{{ trait.symbol }}</td> - <td>{{ trait.alias }}</td> - <td>{{ trait.description }}</td> - <td>Chr{{ trait.chr }}:{{trait.mb}}</td> - <td>{{'%0.3f'|format(trait.mean)}}</td> - <td>{{'%0.3f'|format(trait.lrs)}}</td> - <td>Chr{{ trait.locus_chr }}:{{'%0.6f'|format(trait.locus_mb)}}</td> - <td>{{'%0.3f'|format(trait.sample_r)}}</td> - <td>{{ trait.num_overlap }}</td> - <td>{{'%0.3e'|format(trait.sample_p)}}</td> - <td>{{'%0.3f'|format(trait.lit_corr)}}</td> - <td>{{'%0.3f'|format(trait.tissue_corr)}}</td> - <td>{{'%0.3e'|format(trait.tissue_pvalue)}}</td> - </tr> - {% endfor %} - </tbody> - </table> + <br /> + +<!-- <button class="btn"><i class="icon-ok"></i> Select</button> + <button class="btn"><i class="icon-remove"></i> Deselect</button> + <button class="btn"><i class="icon-resize-vertical"></i> Invert</button> + <button class="btn"><i class="icon-plus-sign"></i> Add</button> + <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>--> + </div> + </div> {% endblock %} {% block js %} @@ -92,4 +113,4 @@ console.timeEnd("Creating table"); }); </script> -{% endblock %} \ No newline at end of file +{% endblock %} diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html index 2f268c5a..fe6f3f65 100644 --- a/wqflask/wqflask/templates/quick_search.html +++ b/wqflask/wqflask/templates/quick_search.html @@ -3,15 +3,14 @@ {% block content %} <!-- Start of body --> - {{ header("QuickSearch Results", - 'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }} + {{ header("QuickSearch Results") }} <div class="container"> <div class="page-header"> <h1>Your Search</h1> </div> - <p>We across all data sets to find all records that match:</p> + <p>We searched across all data sets to find all records that match:</p> <ul> {% if search_terms %} @@ -276,7 +275,7 @@ console.time("Creating table"); $('#pheno_results, #mrna_assay_results, #geno_results').dataTable( { //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>", - "sDom": "lTftipr", + //"sDom": "lTftipr", "oTableTools": { "aButtons": [ "copy", diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index b29e6482..5bd6534c 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -10,7 +10,7 @@ <h1>Your Search</h1> </div> - <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a><//> + <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a></p> <p>To find all records that match:</p> <ul> @@ -85,7 +85,6 @@ <button class="btn" id="add"><i class="icon-plus-sign"></i> Add</button> <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button> </div> - </div> <div id="myModal"></div> diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index e3c84de7..5d77750c 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -2,6 +2,7 @@ {% block title %}Trait Data and Analysis{% endblock %} {% block css %} <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/bar_chart.css" /> <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" /> {% endblock %} @@ -28,7 +29,7 @@ </div> {% include 'show_trait_details.html' %} - {# {% include 'show_trait_statistics.html' %} #} + {% include 'show_trait_statistics_new.html' %} {% include 'show_trait_calculate_correlations.html' %} {% include 'show_trait_mapping_tools.html' %} {% include 'show_trait_edit_data.html' %} diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html new file mode 100644 index 00000000..105c4f95 --- /dev/null +++ b/wqflask/wqflask/templates/show_trait_statistics_new.html @@ -0,0 +1,29 @@ +<div> + <br> + <h2>Charts and Figures</h2> + <div class="well form-horizontal"> + {% if sample_groups|length > 1 %} + <select class="stats_samples_group"> + {% for group, pretty_group in sample_group_types.items() %} + <option value="{{ group }}">{{ pretty_group }}</option> + {% endfor %} + </select> + {% endif %} + {% if sample_groups[0].attributes %} + <div class="input-append"> + <select id="color_attribute" size=1> + <option value="None">None</option> + {% 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> + </div> + {% endif %} + <button type="button" id="update_bar_chart">Sort By Value</button> + <div id="bar_chart_container"> + <div id="bar_chart"></div> + </div> + + </div> +</div> \ No newline at end of file diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 6c9addbc..22973045 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -32,6 +32,7 @@ from base.data_set import create_datasets_list from wqflask.show_trait import show_trait from wqflask.show_trait import export_trait_data from wqflask.marker_regression import marker_regression +#from wqflask.interval_mapping import interval_mapping from wqflask.correlation import show_corr_results from utility import temp_data @@ -247,6 +248,49 @@ def marker_regression_page(): return rendered_template +@app.route("/interval_mapping", methods=('POST',)) +def interval_mapping_page(): + initial_start_vars = request.form + temp_uuid = initial_start_vars['temp_uuid'] + wanted = ( + 'trait_id', + 'dataset', + 'suggestive' + ) + + start_vars = {} + for key, value in initial_start_vars.iteritems(): + if key in wanted or key.startswith(('value:')): + start_vars[key] = value + + version = "v1" + key = "interval_mapping:{}:".format(version) + json.dumps(start_vars, sort_keys=True) + print("key is:", pf(key)) + with Bench("Loading cache"): + result = Redis.get(key) + + if result: + print("Cache hit!!!") + with Bench("Loading results"): + result = pickle.loads(result) + else: + print("Cache miss!!!") + template_vars = interval_mapping.IntervalMapping(start_vars, temp_uuid) + + template_vars.js_data = json.dumps(template_vars.js_data, + default=json_default_handler, + indent=" ") + + result = template_vars.__dict__ + + #causeerror + Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) + Redis.expire(key, 60*60) + + with Bench("Rendering template"): + rendered_template = render_template("interval_mapping.html", **result) + + return rendered_template @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): |