diff options
5 files changed, 108 insertions, 90 deletions
diff --git a/wqflask/wqflask/my_pylmm/data/genofile_parser.py b/wqflask/wqflask/my_pylmm/data/genofile_parser.py index 4a647959..af855fb4 100644 --- a/wqflask/wqflask/my_pylmm/data/genofile_parser.py +++ b/wqflask/wqflask/my_pylmm/data/genofile_parser.py @@ -93,12 +93,12 @@ class ConvertGenoFile(object): this_marker = Marker() this_marker.name = row_items[1] this_marker.chr = row_items[0] - this_marker.cM = row_items[2] + #this_marker.cM = row_items[2] if self.mb_exists: - this_marker.Mb = row_items[3] - genotypes = row_items[4:] - else: + this_marker.Mb = row_items[2] genotypes = row_items[3:] + else: + genotypes = row_items[2:] for item_count, genotype in enumerate(genotypes): if genotype.upper() in self.configurations: this_marker.genotypes.append(self.configurations[genotype.upper()]) @@ -186,8 +186,10 @@ if __name__=="__main__": Old_Geno_Directory = """/home/zas1024/gene/web/genotypes/""" New_Geno_Directory = """/home/zas1024/gene/web/new_genotypes/""" #Input_File = """/home/zas1024/gene/web/genotypes/BXD.geno""" - #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps""" - ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) + #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps""" + convertob = ConvertGenoFile("/home/zas1024/gene/web/genotypes/HSNIH.geno.gz", "/home/zas1024/gene/web/new_genotypes/HSNIH.json") + convertob.convert() + #ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) #ConvertGenoFiles(Geno_Directory) #process_csv(Input_File, Output_File) \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.coffee b/wqflask/wqflask/static/new/javascript/bar_chart.coffee index e1bb36e1..27a8d284 100644 --- a/wqflask/wqflask/static/new/javascript/bar_chart.coffee +++ b/wqflask/wqflask/static/new/javascript/bar_chart.coffee @@ -129,83 +129,12 @@ class Bar_Chart #$('.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", => @open_trait_selection() ) - rebuild_bar_graph: (samples) -> console.log("samples:", samples) @svg.selectAll(".bar") @@ -223,7 +152,11 @@ class Bar_Chart return d[1] ) .style("fill", (d) => - if @attributes.length > 0 and @attribute != "None" + if @attributes.length == 0 + console.log("SAMPLE:", d[0]) + console.log("CHECKING:", @trait_color_dict[d[0]]) + return @trait_color_dict[d[0]] + else 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]]) @@ -231,6 +164,10 @@ class Bar_Chart else return "steelblue" ) + #.style("fill", (d) => + # return @trait_color_dict[d[0]] + # #return @attr_color_dict["collection_trait"][trimmed_samples[d[0]]] + #) sample_names = (sample[0] for sample in samples) console.log("sample_names2:", sample_names) x_scale = d3.scale.ordinal() @@ -268,6 +205,35 @@ class Bar_Chart #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 + + get_trait_color_dict: (samples, vals) -> + @trait_color_dict = {} + console.log("vals:", vals) + for own key, distinct_vals of vals + this_color_dict = {} + if distinct_vals.length < 10 + color = d3.scale.category10() + for value, i in distinct_vals + 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 + else + return true + ) + color_range = d3.scale.linear() + .domain([d3.min(distinct_vals), + d3.max(distinct_vals)]) + .range([0,255]) + for value, i in distinct_vals + console.log("color_range(value):", parseInt(color_range(value))) + this_color_dict[value] = d3.rgb(parseInt(color_range(value)),0, 0) + for own sample, value of samples + @trait_color_dict[sample] = this_color_dict[value] convert_into_colors: (values) -> color_range = d3.scale.linear() @@ -450,14 +416,17 @@ class Bar_Chart trimmed_samples = @trim_values(trait_sample_data) distinct_values = {} distinct_values["collection_trait"] = @get_distinct_values(trimmed_samples) - @get_attr_color_dict(distinct_values) + #@get_attr_color_dict(distinct_values) + @get_trait_color_dict(trimmed_samples, distinct_values) + console.log("TRAIT_COLOR_DICT:", @trait_color_dict) 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]]] + return @trait_color_dict[d[0]] + #return @attr_color_dict["collection_trait"][trimmed_samples[d[0]]] ) .select("title") .text((d) => @@ -469,10 +438,11 @@ class Bar_Chart .transition() .duration(1000) .style("fill", (d) => - return @attr_color_dict["collection_trait"][trimmed_samples[d[0]]] + return @trait_color_dict[d[0]] + #return @attr_color_dict["collection_trait"][trimmed_samples[d[0]]] ) - - + + trim_values: (trait_sample_data) -> trimmed_samples = {} for sample in @sample_names diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.js b/wqflask/wqflask/static/new/javascript/bar_chart.js index b02ee1da..faf66cd4 100644 --- a/wqflask/wqflask/static/new/javascript/bar_chart.js +++ b/wqflask/wqflask/static/new/javascript/bar_chart.js @@ -102,7 +102,11 @@ }).select("title").text(function(d) { return d[1]; }).style("fill", function(d) { - if (_this.attributes.length > 0 && _this.attribute !== "None") { + if (_this.attributes.length === 0) { + console.log("SAMPLE:", d[0]); + console.log("CHECKING:", _this.trait_color_dict[d[0]]); + return _this.trait_color_dict[d[0]]; + } else 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]]); @@ -164,6 +168,48 @@ return _results; }; + Bar_Chart.prototype.get_trait_color_dict = function(samples, vals) { + var color, color_range, distinct_vals, i, key, sample, this_color_dict, value, _i, _j, _len, _len1, _results, + _this = this; + this.trait_color_dict = {}; + console.log("vals:", vals); + 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(); + for (i = _i = 0, _len = distinct_vals.length; _i < _len; i = ++_i) { + value = distinct_vals[i]; + this_color_dict[value] = color(i); + } + } else { + console.log("distinct_values:", distinct_vals); + if (_.every(distinct_vals, function(d) { + if (isNaN(d)) { + return false; + } else { + return true; + } + })) { + 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):", parseInt(color_range(value))); + this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0); + } + } + } + } + _results = []; + for (sample in samples) { + if (!__hasProp.call(samples, sample)) continue; + value = samples[sample]; + _results.push(this.trait_color_dict[sample] = this_color_dict[value]); + } + 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]); @@ -346,16 +392,17 @@ 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); + this.get_trait_color_dict(trimmed_samples, distinct_values); + console.log("TRAIT_COLOR_DICT:", this.trait_color_dict); 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]]]; + return _this.trait_color_dict[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]]]; + return _this.trait_color_dict[d[0]]; }); } }; diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html index e4e08388..e4b93bf4 100644 --- a/wqflask/wqflask/templates/interval_mapping.html +++ b/wqflask/wqflask/templates/interval_mapping.html @@ -77,7 +77,6 @@ <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> - <script type="text/javascript" charset="utf-8"> $(document).ready( function () { console.time("Creating table"); diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html index 6d6b1d24..9393e9bd 100644 --- a/wqflask/wqflask/templates/show_trait_statistics_new.html +++ b/wqflask/wqflask/templates/show_trait_statistics_new.html @@ -51,7 +51,7 @@ <div id="bar_chart"></div> </div> </div> - <div class="tab-pane active" id="box_plot_tab"> + <div class="tab-pane" id="box_plot_tab"> {% if sample_groups|length > 1 %} <select class="box_plot_samples_group"> {% for group, pretty_group in sample_group_types.items() %} |