diff options
25 files changed, 599 insertions, 278 deletions
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py index de7a2704..f0985cc2 100755 --- a/wqflask/wqflask/interval_mapping/interval_mapping.py +++ b/wqflask/wqflask/interval_mapping/interval_mapping.py @@ -37,8 +37,6 @@ class IntervalMapping(object): def __init__(self, start_vars, temp_uuid): - print("TESTING!!!") - #Currently only getting trait data for one trait, but will need #to change this to accept multiple traits once the collection page is implemented helper_functions.get_species_dataset_trait(self, start_vars) @@ -57,7 +55,11 @@ class IntervalMapping(object): self.set_options(start_vars) - self.gen_qtl_results(tempdata) + if self.method == "qtl_reaper": + self.gen_reaper_results(tempdata) + else: + self.gen_pylmm_results(tempdata) + #self.gen_qtl_results(tempdata) #Get chromosome lengths for drawing the interval map plot chromosome_mb_lengths = {} @@ -78,6 +80,7 @@ class IntervalMapping(object): #self.plot_scale = start_vars['scale'] #if self.plotScale == 'physic' and not fd.genotype.Mbmap: # self.plotScale = 'morgan' + self.method = start_vars['mapping_method'] self.num_permutations = int(start_vars['num_permutations']) #self.do_bootstrap = start_vars['do_bootstrap'] self.selected_chr = start_vars['chromosome'] @@ -125,9 +128,6 @@ class IntervalMapping(object): # variance = variances, # control = self.control_locus) #else: - #reaper_results = self.dataset.group.genotype.regression(strains = trimmed_samples, - # trait = trimmed_values, - # control = self.control_locus) reaper_results = genotype.regression(strains = trimmed_samples, trait = trimmed_values, control = self.control_locus) @@ -139,8 +139,6 @@ class IntervalMapping(object): #else: print("strains:", trimmed_samples) print("trait:", trimmed_values) - #reaper_results = self.dataset.group.genotype.regression(strains = trimmed_samples, - # trait = trimmed_values) reaper_results = genotype.regression(strains = trimmed_samples, trait = trimmed_values) @@ -152,29 +150,70 @@ class IntervalMapping(object): qtl = {"lrs": qtl.lrs, "locus": locus, "additive": qtl.additive} self.qtl_results.append(qtl) - #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) + def gen_reaper_results(self, tempdata): + genotype = self.dataset.group.read_genotype_file() + + samples, values, variances = self.this_trait.export_informative() + + trimmed_samples = [] + trimmed_values = [] + for i in range(0, len(samples)): + if samples[i] in self.dataset.group.samplelist: + trimmed_samples.append(samples[i]) + trimmed_values.append(values[i]) + + self.lrs_array = genotype.permutation(strains = trimmed_samples, + trait = trimmed_values, + nperm= self.num_permutations) + self.suggestive = self.lrs_array[int(self.num_permutations*0.37-1)] + self.significant = self.lrs_array[int(self.num_permutations*0.95-1)] + + print("samples:", trimmed_samples) + + if self.control_locus: + reaper_results = genotype.regression(strains = trimmed_samples, + trait = trimmed_values, + control = self.control_locus) + else: + reaper_results = genotype.regression(strains = trimmed_samples, + trait = trimmed_values) + + #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary + self.qtl_results = [] + for qtl in reaper_results: + reaper_locus = qtl.locus + locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb} + qtl = {"lrs_value": qtl.lrs, "chr":reaper_locus.chr, "Mb":reaper_locus.Mb, + "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive} + self.qtl_results.append(qtl) + + def gen_pylmm_results(self, tempdata): + print("USING PYLMM") + self.dataset.group.get_markers() - #self.qtl_results = self.dataset.group.markers.markers + 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 + ) + + print("p_values:", p_values) + 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""" diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 334ce631..006c586b 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -91,7 +91,6 @@ class MarkerRegression(object): ) self.dataset.group.markers.add_pvalues(p_values) - self.qtl_results = self.dataset.group.markers.markers diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 6ef1669b..60d36b8d 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -107,8 +107,6 @@ def run_human(pheno_vector, with Bench("Create list of inputs"): inputs = list(plink_input) - - print("len(genotypes): ", len(inputs)) with Bench("Divide into chunks"): results = chunks.divide_into_chunks(inputs, 64) diff --git a/wqflask/wqflask/static/new/css/interval_mapping.css b/wqflask/wqflask/static/new/css/interval_mapping.css index 9d23ba25..5ebf7742 100644 --- a/wqflask/wqflask/static/new/css/interval_mapping.css +++ b/wqflask/wqflask/static/new/css/interval_mapping.css @@ -1,27 +1,32 @@ -.manhattan_plot .y_axis path, -.manhattan_plot .y_axis line { +.interval_map .y_axis path, +.interval_map .y_axis line { fill: none; stroke: black; shape-rendering: crispEdges; } -.manhattan_plot .y_axis text { +.interval_map .y_axis text { font-family: sans-serif; font-size: 14px; } -.manhattan_plot .x_axis path, -.manhattan_plot .x_axis line { +.interval_map .x_axis path, +.interval_map .x_axis line { fill: none; stroke: black; shape-rendering: crispEdges; } -.manhattan_plot .x_axis text { +.interval_map .x_axis text { text-anchor: end; font-family: sans-serif; font-size: 8px; } -rect { +interval_map rect { stroke: WhiteSmoke; - fill: lightgrey; + fill: white; +} + +interval_map path { + stroke: steelblue; + stroke-width: 1; } \ No newline at end of file diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css index 054ef93e..a737c97e 100644 --- a/wqflask/wqflask/static/new/css/marker_regression.css +++ b/wqflask/wqflask/static/new/css/marker_regression.css @@ -21,10 +21,10 @@ font-size: 8px; } -rect { +/*rect { stroke: WhiteSmoke; fill: lightgrey; -} +}*/ /*rect { stroke: WhiteSmoke; fill: Azure; diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.coffee b/wqflask/wqflask/static/new/javascript/bar_chart.coffee index 412185d8..e1bb36e1 100644 --- a/wqflask/wqflask/static/new/javascript/bar_chart.coffee +++ b/wqflask/wqflask/static/new/javascript/bar_chart.coffee @@ -2,11 +2,12 @@ root = exports ? this class Bar_Chart constructor: (@sample_list, @sample_group) -> + @sort_by = "name" @get_samples() console.log("sample names:", @sample_names) if @sample_attr_vals.length > 0 @get_distinct_attr_vals() - @get_attr_color_dict() + @get_attr_color_dict(@distinct_attr_vals) #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) @@ -28,17 +29,19 @@ class Bar_Chart @create_graph() d3.select("#color_attribute").on("change", => - attribute = $("#color_attribute").val() - if $("#update_bar_chart").html() == 'Sort By Name' + @attribute = $("#color_attribute").val() + console.log("attr_color_dict:", @attr_color_dict) + #if $("#update_bar_chart").html() == 'Sort By Name' + if @sort_by = "name" @svg.selectAll(".bar") .data(@sorted_samples()) .transition() .duration(1000) .style("fill", (d) => - if attribute == "None" + if @attribute == "None" return "steelblue" else - return @attr_color_dict[attribute][d[2][attribute]] + return @attr_color_dict[@attribute][d[2][@attribute]] ) .select("title") .text((d) => @@ -50,86 +53,196 @@ class Bar_Chart .transition() .duration(1000) .style("fill", (d) => - if attribute == "None" + if @attribute == "None" return "steelblue" else - return @attr_color_dict[attribute][d[2][attribute]] + return @attr_color_dict[@attribute][d[2][@attribute]] ) - @add_legend(attribute, @distinct_attr_vals[attribute]) + @add_legend(@attribute, @distinct_attr_vals[@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) + $(".sort_by_value").on("click", => + console.log("sorting by value") + @sort_by = "value" + if @attributes.length > 0 + @attribute = $("#color_attribute").val() + #sortItems = (a, b) -> + # return a[1] - b[1] + @rebuild_bar_graph(@sorted_samples()) + #@svg.selectAll(".bar") + # .data(@sorted_samples()) + # .transition() + # .duration(1000) + # .attr("y", (d) => + # return @y_scale(d[1]) + # ) + # .attr("height", (d) => + # return @plot_height - @y_scale(d[1]) + # ) + # .select("title") + # .text((d) => + # return d[1] + # ) + # #.style("fill", (d) => + # # if @attributes.length > 0 + # # return @attr_color_dict[attribute][d[2][attribute]] + # # else + # # return "steelblue" + # #) + #sorted_sample_names = (sample[0] for sample in @sorted_samples()) + #x_scale = d3.scale.ordinal() + # .domain(sorted_sample_names) + # .rangeBands([0, @plot_width], .1) + #$('.x.axis').remove() + #@add_x_axis(x_scale) + ) + + $(".sort_by_name").on("click", => + console.log("sorting by name") + @sort_by = "name" + if @attributes.length > 0 + @attribute = $("#color_attribute").val() + @rebuild_bar_graph(@samples) + #@svg.selectAll(".bar") + # .data(@samples) + # .transition() + # .duration(1000) + # .attr("y", (d) => + # return @y_scale(d[1]) + # ) + # .attr("height", (d) => + # return @plot_height - @y_scale(d[1]) + # ) + # .select("title") + # .text((d) => + # return d[1] + # ) + # .style("fill", (d) => + # if @attributes.length > 0 + # return @attr_color_dict[attribute][d[2][attribute]] + # else + # return "steelblue" + # ) + #x_scale = d3.scale.ordinal() + # .domain(@sample_names) + # .rangeBands([0, @plot_width], .1) + #$('.x.axis').remove() + #@add_x_axis(x_scale) ) + + + #d3.select(".update_bar_chart").on("click", => + # console.log("THIS IS:", $(this)) + # sort_by = $(this).val() + # console.log("sort_by: ", sort_by) + # if @attributes.length > 0 + # attribute = $("#color_attribute").val() + # if sort_by = "value" + # console.log("sorting by value") + # 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) + # $('.x.axis').remove() + # @add_x_axis(x_scale) + # else + # console.log("sorting by name") + # #$("#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) + #) + d3.select("#color_by_trait").on("click", => - @color_by_trait() + @open_trait_selection() + ) - get_attr_color_dict: () -> + + rebuild_bar_graph: (samples) -> + console.log("samples:", samples) + @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]) + ) + .select("title") + .text((d) => + return d[1] + ) + .style("fill", (d) => + if @attributes.length > 0 and @attribute != "None" + console.log("@attribute:", @attribute) + console.log("d[2]", d[2]) + console.log("the_color:", @attr_color_dict[@attribute][d[2][@attribute]]) + return @attr_color_dict[@attribute][d[2][@attribute]] + else + return "steelblue" + ) + sample_names = (sample[0] for sample in samples) + console.log("sample_names2:", sample_names) + 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: (vals) -> @attr_color_dict = {} - console.log("distinct_attr_vals:", @distinct_attr_vals) - for own key, distinct_vals of @distinct_attr_vals + console.log("vals:", vals) + for own key, distinct_vals of vals this_color_dict = {} if distinct_vals.length < 10 color = d3.scale.category10() @@ -137,6 +250,8 @@ class Bar_Chart this_color_dict[value] = color(i) else console.log("distinct_values:", distinct_vals) + #Check whether all values are numbers, and if they are get a corresponding + #color gradient if _.every(distinct_vals, (d) => if isNaN(d) return false @@ -146,13 +261,24 @@ class Bar_Chart color_range = d3.scale.linear() .domain([d3.min(distinct_vals), d3.max(distinct_vals)]) - .range([0,4]) + .range([0,255]) for value, i in distinct_vals - console.log("color_range(value):", color_range(parseInt(value))) - this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value))) + console.log("color_range(value):", parseInt(color_range(value))) + this_color_dict[value] = d3.rgb(parseInt(color_range(value)),0, 0) + #this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value))) #this_color_dict[value] = "rgb(0, 0, " + color_range(parseInt(value)) + ")" @attr_color_dict[key] = this_color_dict + convert_into_colors: (values) -> + color_range = d3.scale.linear() + .domain([d3.min(values), + d3.max(values)]) + .range([0,255]) + for value, i in values + console.log("color_range(value):", color_range(parseInt(value))) + this_color_dict[value] = d3.rgb(color_range(parseInt(value)),0, 0) + #this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value))) + 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) @@ -304,7 +430,7 @@ class Bar_Chart return d ) - color_by_trait: () -> + open_trait_selection: () -> $('#collections_holder').load('/collections/list?color_by_trait #collections_list', => $.colorbox( inline: true @@ -317,6 +443,50 @@ class Bar_Chart # console.log("contents:", $(element).contents()) # $(element).contents().unwrap() ) + + color_by_trait: (trait_sample_data) -> + console.log("BXD1:", trait_sample_data["BXD1"]) + console.log("trait_sample_data:", trait_sample_data) + trimmed_samples = @trim_values(trait_sample_data) + distinct_values = {} + distinct_values["collection_trait"] = @get_distinct_values(trimmed_samples) + @get_attr_color_dict(distinct_values) + if $("#update_bar_chart").html() == 'Sort By Name' + @svg.selectAll(".bar") + .data(@sorted_samples()) + .transition() + .duration(1000) + .style("fill", (d) => + return @attr_color_dict["collection_trait"][trimmed_samples[d[0]]] + ) + .select("title") + .text((d) => + return d[1] + ) + else + @svg.selectAll(".bar") + .data(@samples) + .transition() + .duration(1000) + .style("fill", (d) => + return @attr_color_dict["collection_trait"][trimmed_samples[d[0]]] + ) + + + trim_values: (trait_sample_data) -> + trimmed_samples = {} + for sample in @sample_names + if sample of trait_sample_data + trimmed_samples[sample] = trait_sample_data[sample] + console.log("trimmed_samples:", trimmed_samples) + return trimmed_samples + get_distinct_values: (samples) -> + distinct_values = _.uniq(_.values(samples)) + console.log("distinct_values:", distinct_values) + return distinct_values + #distinct_values = [] + #for sample in samples + # if samples[sample] in distinct_values root.Bar_Chart = Bar_Chart \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.js b/wqflask/wqflask/static/new/javascript/bar_chart.js index e4279d41..b02ee1da 100644 --- a/wqflask/wqflask/static/new/javascript/bar_chart.js +++ b/wqflask/wqflask/static/new/javascript/bar_chart.js @@ -13,11 +13,12 @@ _this = this; this.sample_list = sample_list; this.sample_group = sample_group; + this.sort_by = "name"; this.get_samples(); console.log("sample names:", this.sample_names); if (this.sample_attr_vals.length > 0) { this.get_distinct_attr_vals(); - this.get_attr_color_dict(); + this.get_attr_color_dict(this.distinct_attr_vals); } longest_sample_name = d3.max((function() { var _i, _len, _ref, _results; @@ -46,100 +47,94 @@ 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') { + _this.attribute = $("#color_attribute").val(); + console.log("attr_color_dict:", _this.attr_color_dict); + if (_this.sort_by = "name") { _this.svg.selectAll(".bar").data(_this.sorted_samples()).transition().duration(1000).style("fill", function(d) { - if (attribute === "None") { + if (_this.attribute === "None") { return "steelblue"; } else { - return _this.attr_color_dict[attribute][d[2][attribute]]; + return _this.attr_color_dict[_this.attribute][d[2][_this.attribute]]; } }).select("title").text(function(d) { return d[1]; }); } else { _this.svg.selectAll(".bar").data(_this.samples).transition().duration(1000).style("fill", function(d) { - if (attribute === "None") { + if (_this.attribute === "None") { return "steelblue"; } else { - return _this.attr_color_dict[attribute][d[2][attribute]]; + return _this.attr_color_dict[_this.attribute][d[2][_this.attribute]]; } }); } - return _this.add_legend(attribute, _this.distinct_attr_vals[attribute]); + return _this.add_legend(_this.attribute, _this.distinct_attr_vals[_this.attribute]); }); - d3.select("#update_bar_chart").on("click", function() { - var attribute, sortItems, sorted_sample_names, x_scale; + $(".sort_by_value").on("click", function() { + console.log("sorting by value"); + _this.sort_by = "value"; if (_this.attributes.length > 0) { - attribute = $("#color_attribute").val(); + _this.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); + return _this.rebuild_bar_graph(_this.sorted_samples()); + }); + $(".sort_by_name").on("click", function() { + console.log("sorting by name"); + _this.sort_by = "name"; + if (_this.attributes.length > 0) { + _this.attribute = $("#color_attribute").val(); } + return _this.rebuild_bar_graph(_this.samples); }); d3.select("#color_by_trait").on("click", function() { - return _this.color_by_trait(); + return _this.open_trait_selection(); }); } - Bar_Chart.prototype.get_attr_color_dict = function() { - var color, color_range, distinct_vals, i, key, this_color_dict, value, _i, _j, _len, _len1, _ref, _results, + Bar_Chart.prototype.rebuild_bar_graph = function(samples) { + var sample, sample_names, x_scale, + _this = this; + console.log("samples:", samples); + this.svg.selectAll(".bar").data(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]); + }).select("title").text(function(d) { + return d[1]; + }).style("fill", function(d) { + if (_this.attributes.length > 0 && _this.attribute !== "None") { + console.log("@attribute:", _this.attribute); + console.log("d[2]", d[2]); + console.log("the_color:", _this.attr_color_dict[_this.attribute][d[2][_this.attribute]]); + return _this.attr_color_dict[_this.attribute][d[2][_this.attribute]]; + } else { + return "steelblue"; + } + }); + sample_names = (function() { + var _i, _len, _results; + _results = []; + for (_i = 0, _len = samples.length; _i < _len; _i++) { + sample = samples[_i]; + _results.push(sample[0]); + } + return _results; + })(); + console.log("sample_names2:", sample_names); + x_scale = d3.scale.ordinal().domain(sample_names).rangeBands([0, this.plot_width], .1); + $('.x.axis').remove(); + return this.add_x_axis(x_scale); + }; + + Bar_Chart.prototype.get_attr_color_dict = function(vals) { + var color, color_range, distinct_vals, i, key, this_color_dict, value, _i, _j, _len, _len1, _results, _this = this; this.attr_color_dict = {}; - console.log("distinct_attr_vals:", this.distinct_attr_vals); - _ref = this.distinct_attr_vals; + console.log("vals:", vals); _results = []; - for (key in _ref) { - if (!__hasProp.call(_ref, key)) continue; - distinct_vals = _ref[key]; + for (key in vals) { + if (!__hasProp.call(vals, key)) continue; + distinct_vals = vals[key]; this_color_dict = {}; if (distinct_vals.length < 10) { color = d3.scale.category10(); @@ -156,11 +151,11 @@ return true; } })) { - color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 4]); + color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 255]); for (i = _j = 0, _len1 = distinct_vals.length; _j < _len1; i = ++_j) { value = distinct_vals[i]; - console.log("color_range(value):", color_range(parseInt(value))); - this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value))); + console.log("color_range(value):", parseInt(color_range(value))); + this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0); } } } @@ -169,6 +164,18 @@ return _results; }; + Bar_Chart.prototype.convert_into_colors = function(values) { + var color_range, i, value, _i, _len, _results; + color_range = d3.scale.linear().domain([d3.min(values), d3.max(values)]).range([0, 255]); + _results = []; + for (i = _i = 0, _len = values.length; _i < _len; i = ++_i) { + value = values[i]; + console.log("color_range(value):", color_range(parseInt(value))); + _results.push(this_color_dict[value] = d3.rgb(color_range(parseInt(value)), 0, 0)); + } + return _results; + }; + Bar_Chart.prototype.get_samples = function() { var attr_vals, attribute, key, sample, _i, _j, _len, _len1, _ref, _ref1; this.sample_names = (function() { @@ -320,7 +327,7 @@ }); }; - Bar_Chart.prototype.color_by_trait = function() { + Bar_Chart.prototype.open_trait_selection = function() { var _this = this; return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', function() { $.colorbox({ @@ -331,6 +338,49 @@ }); }; + Bar_Chart.prototype.color_by_trait = function(trait_sample_data) { + var distinct_values, trimmed_samples, + _this = this; + console.log("BXD1:", trait_sample_data["BXD1"]); + console.log("trait_sample_data:", trait_sample_data); + trimmed_samples = this.trim_values(trait_sample_data); + distinct_values = {}; + distinct_values["collection_trait"] = this.get_distinct_values(trimmed_samples); + this.get_attr_color_dict(distinct_values); + if ($("#update_bar_chart").html() === 'Sort By Name') { + return this.svg.selectAll(".bar").data(this.sorted_samples()).transition().duration(1000).style("fill", function(d) { + return _this.attr_color_dict["collection_trait"][trimmed_samples[d[0]]]; + }).select("title").text(function(d) { + return d[1]; + }); + } else { + return this.svg.selectAll(".bar").data(this.samples).transition().duration(1000).style("fill", function(d) { + return _this.attr_color_dict["collection_trait"][trimmed_samples[d[0]]]; + }); + } + }; + + Bar_Chart.prototype.trim_values = function(trait_sample_data) { + var sample, trimmed_samples, _i, _len, _ref; + trimmed_samples = {}; + _ref = this.sample_names; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + sample = _ref[_i]; + if (sample in trait_sample_data) { + trimmed_samples[sample] = trait_sample_data[sample]; + } + } + console.log("trimmed_samples:", trimmed_samples); + return trimmed_samples; + }; + + Bar_Chart.prototype.get_distinct_values = function(samples) { + var distinct_values; + distinct_values = _.uniq(_.values(samples)); + console.log("distinct_values:", distinct_values); + return distinct_values; + }; + return Bar_Chart; })(); diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee b/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee index 16590e26..af53bd09 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee @@ -104,7 +104,7 @@ $ -> defaults = species: "mouse" group: "BXD" - type: "Hippocampus" + type: "Hippocampus mRNA" dataset: "HC_M2_0606_P" for item in [['species', 'group'] diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js index 5c5b433a..3a2f044f 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js @@ -111,7 +111,7 @@ defaults = { species: "mouse", group: "BXD", - type: "Hippocampus", + type: "Hippocampus mRNA", dataset: "HC_M2_0606_P" }; } diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee index f1d41cbe..db398809 100644 --- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee +++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee @@ -1,9 +1,11 @@ +root = exports ? this console.log("before get_traits_from_collection") # Going to be used to hold collection list # So we can repopulate it when the back button is clicked collection_list = null +this_trait_data = null collection_click = () -> console.log("Clicking on:", $(this)) @@ -16,7 +18,7 @@ collection_click = () -> url: this_collection_url, success: process_traits ) - + trait_click = () -> console.log("Clicking on:", $(this)) trait = $(this).find('.trait').text() @@ -28,9 +30,12 @@ trait_click = () -> url: this_trait_url, success: color_by_trait ) + $.colorbox.close() color_by_trait = (trait_sample_data, textStatus, jqXHR) -> - console.log('in color_by_trait:', trait_sample_data) + #trait_sample_data = trait_sample_data + #console.log('in color_by_trait:', trait_sample_data) + root.bar_chart.color_by_trait(trait_sample_data) process_traits = (trait_data, textStatus, jqXHR) -> console.log('in process_traits with trait_data:', trait_data) @@ -65,3 +70,4 @@ $ -> $(document).on("click", ".collection_line", collection_click) $(document).on("click", ".trait_line", trait_click) $(document).on("click", "#back_to_collections", back_to_collections) + diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js index 104c411d..fac543f8 100644 --- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js +++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js @@ -1,11 +1,15 @@ // Generated by CoffeeScript 1.6.1 (function() { - var back_to_collections, collection_click, collection_list, color_by_trait, process_traits, trait_click; + var back_to_collections, collection_click, collection_list, color_by_trait, process_traits, root, this_trait_data, trait_click; + + root = typeof exports !== "undefined" && exports !== null ? exports : this; console.log("before get_traits_from_collection"); collection_list = null; + this_trait_data = null; + collection_click = function() { var this_collection_url; console.log("Clicking on:", $(this)); @@ -34,8 +38,10 @@ }); }; + $.colorbox.close(); + color_by_trait = function(trait_sample_data, textStatus, jqXHR) { - return console.log('in color_by_trait:', trait_sample_data); + return root.bar_chart.color_by_trait(trait_sample_data); }; process_traits = function(trait_data, textStatus, jqXHR) { diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.coffee b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee index 78265f27..81db186b 100644 --- a/wqflask/wqflask/static/new/javascript/interval_mapping.coffee +++ b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee @@ -66,30 +66,30 @@ $ -> chr_lengths.push(this_length) cumulative_chr_lengths.push(total_length + this_length) total_length += this_length - + console.log("chr_lengths: ", chr_lengths) - + return [chr_lengths, cumulative_chr_lengths] - + create_coordinates: () -> chr_lengths = [] chr_seen = [] for result in js_data.qtl_results - if result.locus.chr == "X" + if result.chr == "X" chr_length = parseFloat(@chromosomes[20]) else - chr_length = parseFloat(@chromosomes[result.locus.chr]) - if not(result.locus.chr in chr_seen) - chr_seen.push(result.locus.chr) + chr_length = parseFloat(@chromosomes[result.chr]) + if not(result.chr in chr_seen) + chr_seen.push(result.chr) chr_lengths.push(chr_length) - if result.locus.chr != "1" + if result.chr != "1" @total_length += parseFloat(chr_lengths[chr_lengths.length - 2]) - @x_coords.push(@total_length + parseFloat(result.locus.Mb)) - @y_coords.push(result.lrs) - @marker_names.push(result.locus.name) + @x_coords.push(@total_length + parseFloat(result.Mb)) + @y_coords.push(result.lrs_value) + @marker_names.push(result.name) @total_length += parseFloat(chr_lengths[chr_lengths.length-1]) #console.log("chr_lengths: ", chr_lengths) - + create_svg: () -> svg = d3.select("#interval_map") .append("svg") @@ -98,7 +98,7 @@ $ -> .attr("height", @plot_height+@y_buffer) return svg - + create_graph: () -> @add_border() @add_x_axis() @@ -107,13 +107,13 @@ $ -> @fill_chr_areas() @add_chr_labels() @connect_markers() - + add_border: () -> border_coords = [[@y_buffer, @plot_height, @x_buffer, @x_buffer], [@y_buffer, @plot_height, @plot_width, @plot_width], [@y_buffer, @y_buffer, @x_buffer, @plot_width], [@plot_height, @plot_height, @x_buffer, @plot_width]] - + @svg.selectAll("line") .data(border_coords) .enter() @@ -131,16 +131,16 @@ $ -> return d[3] ) .style("stroke", "#000") - + create_scales: () -> @x_scale = d3.scale.linear() .domain([0, d3.max(@x_coords)]) .range([@x_buffer, @plot_width]) - + @y_scale = d3.scale.linear() .domain([0, @y_max]) .range([@plot_height, @y_buffer]) - + create_x_axis_tick_values: () -> tick_vals = [] for val in [25..@cumulative_chr_lengths[0]] when val%25 == 0 @@ -159,13 +159,13 @@ $ -> #console.log("tick_vals:", tick_vals) return tick_vals - + add_x_axis: () -> xAxis = d3.svg.axis() .scale(@x_scale) .orient("bottom") .tickValues(@create_x_axis_tick_values()) - + next_chr = 1 tmp_tick_val = 0 xAxis.tickFormat((d) => @@ -183,7 +183,7 @@ $ -> tick_val = tmp_tick_val return (tick_val) ) - + @svg.append("g") .attr("class", "x_axis") .attr("transform", "translate(0," + @plot_height + ")") @@ -196,7 +196,7 @@ $ -> ) #.attr("dy", "-1.0em") - + add_y_axis: () -> yAxis = d3.svg.axis() .scale(@y_scale) @@ -207,7 +207,7 @@ $ -> .attr("class", "y_axis") .attr("transform", "translate(" + @x_buffer + ",0)") .call(yAxis) - + add_chr_lines: () -> @svg.selectAll("line") .data(@cumulative_chr_lengths, (d) => @@ -215,10 +215,10 @@ $ -> ) .enter() .append("line") - .attr("x1", @x_scale) - .attr("x2", @x_scale) .attr("y1", @y_buffer) .attr("y2", @plot_height) + .attr("x1", @x_scale) + .attr("x2", @x_scale) .style("stroke", "#ccc") fill_chr_areas: () -> @@ -239,8 +239,9 @@ $ -> .attr("width", (d) => return @x_scale(d[0]) ) - .attr("height", @plot_height-@y_buffer) - + .attr("height", @plot_height-@y_buffer) + .attr("fill", "white") + add_chr_labels: () -> chr_names = [] for key of @chromosomes @@ -263,12 +264,13 @@ $ -> .attr("text-anchor", "middle") .attr("font-family", "sans-serif") .attr("font-size", "18px") - .attr("fill", "grey") - + #.attr("fill", "grey") + connect_markers: () -> - @svg.selectAll("path") + @svg.selectAll("line") .data(@plot_coordinates) .enter() + .append("line") .attr("x1", (d, i) => if i == 0 return @x_buffer @@ -287,7 +289,9 @@ $ -> .attr("y2", (d) => return @plot_height - ((@plot_height-@y_buffer) * d[1]/@y_max) ) - - console.time('Create manhattan plot') + .style("stroke", "black") + + console.time('Create interval map') + console.log("TESTING") new Interval_Map(600, 1200) - console.timeEnd('Create manhattan plot') \ No newline at end of file + console.timeEnd('Create interval map') \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.js b/wqflask/wqflask/static/new/javascript/interval_mapping.js index 5ae8ffab..3a2ce6d7 100644 --- a/wqflask/wqflask/static/new/javascript/interval_mapping.js +++ b/wqflask/wqflask/static/new/javascript/interval_mapping.js @@ -85,21 +85,21 @@ _ref = js_data.qtl_results; for (_i = 0, _len = _ref.length; _i < _len; _i++) { result = _ref[_i]; - if (result.locus.chr === "X") { + if (result.chr === "X") { chr_length = parseFloat(this.chromosomes[20]); } else { - chr_length = parseFloat(this.chromosomes[result.locus.chr]); + chr_length = parseFloat(this.chromosomes[result.chr]); } - if (!(_ref1 = result.locus.chr, __indexOf.call(chr_seen, _ref1) >= 0)) { - chr_seen.push(result.locus.chr); + if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) { + chr_seen.push(result.chr); chr_lengths.push(chr_length); - if (result.locus.chr !== "1") { + if (result.chr !== "1") { this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]); } } - this.x_coords.push(this.total_length + parseFloat(result.locus.Mb)); - this.y_coords.push(result.lrs); - this.marker_names.push(result.locus.name); + this.x_coords.push(this.total_length + parseFloat(result.Mb)); + this.y_coords.push(result.lrs_value); + this.marker_names.push(result.name); } return this.total_length += parseFloat(chr_lengths[chr_lengths.length - 1]); }; @@ -205,7 +205,7 @@ var _this = this; return this.svg.selectAll("line").data(this.cumulative_chr_lengths, function(d) { return d; - }).enter().append("line").attr("x1", this.x_scale).attr("x2", this.x_scale).attr("y1", this.y_buffer).attr("y2", this.plot_height).style("stroke", "#ccc"); + }).enter().append("line").attr("y1", this.y_buffer).attr("y2", this.plot_height).attr("x1", this.x_scale).attr("x2", this.x_scale).style("stroke", "#ccc"); }; Interval_Map.prototype.fill_chr_areas = function() { @@ -220,7 +220,7 @@ } }).attr("y", this.y_buffer).attr("width", function(d) { return _this.x_scale(d[0]); - }).attr("height", this.plot_height - this.y_buffer); + }).attr("height", this.plot_height - this.y_buffer).attr("fill", "white"); }; Interval_Map.prototype.add_chr_labels = function() { @@ -237,12 +237,12 @@ return d[0]; }).attr("x", function(d) { return _this.x_scale(d[2] - d[1] / 2); - }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "grey"); + }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px"); }; Interval_Map.prototype.connect_markers = function() { var _this = this; - return this.svg.selectAll("path").data(this.plot_coordinates).enter().attr("x1", function(d, i) { + return this.svg.selectAll("line").data(this.plot_coordinates).enter().append("line").attr("x1", function(d, i) { if (i === 0) { return _this.x_buffer; } else { @@ -258,15 +258,16 @@ return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * d[0] / parseFloat(_this.x_max)); }).attr("y2", function(d) { return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max); - }); + }).style("stroke", "black"); }; return Interval_Map; })(); - console.time('Create manhattan plot'); + console.time('Create interval map'); + console.log("TESTING"); new Interval_Map(600, 1200); - return console.timeEnd('Create manhattan plot'); + return console.timeEnd('Create interval map'); }); }).call(this); diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee index 2892987e..f5f13c27 100644 --- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee +++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee @@ -49,10 +49,10 @@ $ -> get_chr_lengths: () -> ### - Gets a list of both individual and cumulative (the position of one on the graph - is its own length plus the lengths of all preceding chromosomes) lengths in order - to draw the vertical lines separating chromosomes and the chromosome labels - + #Gets a list of both individual and cumulative (the position of one on the graph + #is its own length plus the lengths of all preceding chromosomes) lengths in order + #to draw the vertical lines separating chromosomes and the chromosome labels + # ### console.log("@chromosomes: ", @chromosomes) diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js index ffcf1a75..cdf37671 100644 --- a/wqflask/wqflask/static/new/javascript/marker_regression.js +++ b/wqflask/wqflask/static/new/javascript/marker_regression.js @@ -57,9 +57,10 @@ Manhattan_Plot.prototype.get_chr_lengths = function() { /* - Gets a list of both individual and cumulative (the position of one on the graph - is its own length plus the lengths of all preceding chromosomes) lengths in order - to draw the vertical lines separating chromosomes and the chromosome labels + #Gets a list of both individual and cumulative (the position of one on the graph + #is its own length plus the lengths of all preceding chromosomes) lengths in order + #to draw the vertical lines separating chromosomes and the chromosome labels + # */ var chr_lengths, cumulative_chr_lengths, key, this_length, total_length; diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index 7d23345f..1df033d6 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -1,3 +1,5 @@ +root = exports ? this + console.log("start_b") # this is our isNumber, do not confuse with the underscore.js one @@ -62,10 +64,10 @@ $ -> sample_lists = js_data.sample_lists sample_group_types = js_data.sample_group_types - new Bar_Chart(sample_lists[0]) + $("#update_bar_chart.btn-group").button() + root.bar_chart = new Bar_Chart(sample_lists[0]) new Box_Plot(sample_lists[0]) - $('.bar_chart_samples_group').change -> $('#bar_chart').remove() $('#bar_chart_container').append('<div id="bar_chart"></div>') @@ -77,7 +79,8 @@ $ -> else if group == "samples_all" all_samples = sample_lists[0].concat sample_lists[1] new Bar_Chart(all_samples) - + #$(".btn-group").button() + $('.box_plot_samples_group').change -> $('#box_plot').remove() $('#box_plot_container').append('<div id="box_plot"></div>') diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 718e365a..90fa8228 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -1,9 +1,11 @@ // Generated by CoffeeScript 1.6.1 (function() { - var Stat_Table_Rows, is_number, + var Stat_Table_Rows, is_number, root, __hasProp = {}.hasOwnProperty, __slice = [].slice; + root = typeof exports !== "undefined" && exports !== null ? exports : this; + console.log("start_b"); is_number = function(o) { @@ -59,7 +61,8 @@ 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, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values; sample_lists = js_data.sample_lists; sample_group_types = js_data.sample_group_types; - new Bar_Chart(sample_lists[0]); + $("#update_bar_chart.btn-group").button(); + root.bar_chart = new Bar_Chart(sample_lists[0]); new Box_Plot(sample_lists[0]); $('.bar_chart_samples_group').change(function() { var all_samples, group; diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee index 8571753e..df9bfc9d 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee @@ -53,6 +53,7 @@ $ -> return false $("#interval_mapping_compute").click(() => + console.log("In interval mapping") $("#progress_bar_container").modal() url = "/interval_mapping" form_data = $('#trait_data_form').serialize() @@ -118,8 +119,12 @@ $ -> composite_mapping_fields = -> $(".composite_fields").toggle() + mapping_method_fields = -> + $(".mapping_method_fields").toggle() + $("#use_composite_choice").change(composite_mapping_fields) + $("#mapping_method_choice").change(mapping_method_fields) #### Todo: Redo below so its like submit_special and requires no js hardcoding 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 1153b8ef..b474bd80 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -5,7 +5,7 @@ root = typeof exports !== "undefined" && exports !== null ? exports : this; $(function() { - var composite_mapping_fields, get_progress, submit_special, toggle_enable_disable, update_time_remaining, + var composite_mapping_fields, get_progress, mapping_method_fields, submit_special, toggle_enable_disable, update_time_remaining, _this = this; submit_special = function() { var url; @@ -64,6 +64,7 @@ }; $("#interval_mapping_compute").click(function() { var form_data, url; + console.log("In interval mapping"); $("#progress_bar_container").modal(); url = "/interval_mapping"; form_data = $('#trait_data_form').serialize(); @@ -128,7 +129,11 @@ composite_mapping_fields = function() { return $(".composite_fields").toggle(); }; + mapping_method_fields = function() { + return $(".mapping_method_fields").toggle(); + }; $("#use_composite_choice").change(composite_mapping_fields); + $("#mapping_method_choice").change(mapping_method_fields); toggle_enable_disable = function(elem) { return $(elem).prop("disabled", !$(elem).prop("disabled")); }; diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html index ac621a61..354723d0 100644 --- a/wqflask/wqflask/templates/collections/list.html +++ b/wqflask/wqflask/templates/collections/list.html @@ -35,7 +35,7 @@ </table> {# if "color_by_trait" in params #} - <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script> +<!-- <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>--> {# endif #} </div> diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html index 25de2dc1..e4e08388 100644 --- a/wqflask/wqflask/templates/interval_mapping.html +++ b/wqflask/wqflask/templates/interval_mapping.html @@ -1,7 +1,6 @@ {% extends "base.html" %} {% block title %}Interval Mapping{% endblock %} {% block css %} - <link rel="stylesheet" type="text/css" href="/static/packages/jqplot/jquery.jqplot.min.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.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" /> @@ -31,7 +30,9 @@ <tr> <td>Index</td> <td>LRS Score</td> + {% if method == "qtl_reaper" %} <td>Additive Effect</td> + {% endif %} <td>Chr</td> <td>Mb</td> <td>Locus</td> @@ -41,11 +42,13 @@ {% for marker in qtl_results %} <tr> <td>{{ loop.index }}</td> - <td>{{ marker.lrs|float }}</td> + <td>{{ marker.lrs_value|float }}</td> + {% if method == "qtl_reaper" %} <td>{{ marker.additive|float }}</td> - <td>{{ marker.locus.chr|int }}</td> - <td>{{ marker.locus.Mb|float }}</td> - <td>{{ marker.locus.name }}</td> + {% endif %} + <td>{{ marker.chr|int }}</td> + <td>{{ marker.Mb|float }}</td> + <td>{{ marker.name }}</td> </tr> {% endfor %} </tbody> @@ -63,7 +66,7 @@ </script> <!--[if lt IE 9]> - <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script> +<!-- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>--> <![endif]--> <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/interval_mapping.js"></script> diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index ec729e1c..86891bb0 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/interval_mapping.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/bar_chart.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" /> <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> @@ -55,10 +56,11 @@ <script type="text/javascript" src="/static/new/javascript/stats.js"></script> <script type="text/javascript" src="/static/new/javascript/box.js"></script> + <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script> <script type="text/javascript" src="/static/new/javascript/bar_chart.js"></script> <script type="text/javascript" src="/static/new/javascript/box_plot.js"></script> - <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script> - <script type="text/javascript" src="/static/new/javascript/show_trait.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> {% endblock %} diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index a835a41b..58ee8982 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -17,6 +17,16 @@ <div class="tab-content"> <div class="tab-pane active" id="interval_mapping"> <div class="control-group"> + <label for="mapping_method" class="control-label">Mapping Method</label> + <div class="controls" id="mapping_method_choice"> + <select name="mapping_method"> + <option value="qtl_reaper">H&K Regression</option> + <option value="pylmm">Linear Mixed</option> + </select> + </div> + </div> + + <div class="control-group"> <label for="chromosome" class="control-label">Chromosome</label> <div class="controls"> <select name="chromosome"> @@ -28,14 +38,14 @@ </div> </div> - <div class="control-group"> + <div class="control-group mapping_method_fields"> <label for="mapping_permutations" class="control-label">Permutations (n)</label> <div class="controls"> <input name="num_permutations" value="2000" type="text" /> </div> </div> - <div class="control-group"> + <div class="control-group mapping_method_fields"> <label for="mapping_bootstraps" class="control-label" title="Bootstrapping Resamples">Bootstrap (n)</label> <div class="controls"> @@ -44,7 +54,7 @@ </div> - <div class="control-group"> + <div class="control-group mapping_method_fields"> <label class="control-label"><b>Composite Mapping</b></label> <div class="controls" id="use_composite_choice"> <label class="radio inline"> diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html index 33538626..6d6b1d24 100644 --- a/wqflask/wqflask/templates/show_trait_statistics_new.html +++ b/wqflask/wqflask/templates/show_trait_statistics_new.html @@ -30,13 +30,23 @@ {% endfor %} </select> </div> - {% endif %} - <button type="button" class="btn" id="update_bar_chart"> + {% endif %} + <div id="update_bar_chart" class="btn-group"> + <button type="button" class="btn btn-default sort_by_name" value="name"> + <i class="icon-resize-horizontal"></i> Sort By Name + </button> + <button type="button" class="btn btn-default sort_by_value" value="value"> + <i class="icon-signal"></i> Sort By Value + </button> + </div> +<!-- <button type="button" class="btn" id="update_bar_chart"> <i class="icon-resize-vertical"></i> Sort By Value - </button> - <button type="button" class="btn" id="color_by_trait"> - <i class="icon-tint"></i> Color by Trait - </button> + </button>--> + <div class="btn-group"> + <button type="button" class="btn" id="color_by_trait"> + <i class="icon-tint"></i> Color by Trait + </button> + </div> <div id="bar_chart_container"> <div id="bar_chart"></div> </div> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index b528f2b1..828199c5 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -258,6 +258,7 @@ def interval_mapping_page(): wanted = ( 'trait_id', 'dataset', + 'mapping_method', 'chromosome', 'num_permutations', 'do_bootstraps', |