diff options
Diffstat (limited to 'wqflask/wqflask/static/new/javascript/chr_lod_chart.js')
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/chr_lod_chart.js | 297 |
1 files changed, 0 insertions, 297 deletions
diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js deleted file mode 100644 index c6cbd01b..00000000 --- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js +++ /dev/null @@ -1,297 +0,0 @@ -// Generated by CoffeeScript 1.9.2 -var Chr_Lod_Chart; - -Chr_Lod_Chart = (function() { - function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot, mappingScale) { - this.plot_height = plot_height; - this.plot_width = plot_width; - this.chr = chr; - this.manhattanPlot = manhattanPlot; - this.mappingScale = mappingScale; - this.qtl_results = js_data.qtl_results; - console.log("qtl_results are:", this.qtl_results); - console.log("chr is:", this.chr); - this.get_max_chr(); - this.filter_qtl_results(); - console.log("filtered results:", this.these_results); - this.get_qtl_count(); - this.x_coords = []; - this.y_coords = []; - this.marker_names = []; - console.time('Create coordinates'); - this.create_coordinates(); - console.log("@x_coords: ", this.x_coords); - console.log("@y_coords: ", this.y_coords); - console.timeEnd('Create coordinates'); - this.x_buffer = this.plot_width / 30; - this.y_buffer = this.plot_height / 20; - this.x_max = d3.max(this.x_coords); - this.y_max = d3.max(this.y_coords) * 1.2; - this.y_threshold = this.get_lod_threshold(); - this.svg = this.create_svg(); - this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names); - console.log("coordinates:", this.plot_coordinates); - this.plot_height -= this.y_buffer; - this.create_scales(); - console.time('Create graph'); - this.create_graph(); - console.timeEnd('Create graph'); - } - - Chr_Lod_Chart.prototype.get_max_chr = function() { - var key, results; - this.max_chr = 0; - results = []; - for (key in js_data.chromosomes) { - console.log("key is:", key); - if (parseInt(key) > this.max_chr) { - results.push(this.max_chr = parseInt(key)); - } else { - results.push(void 0); - } - } - return results; - }; - - Chr_Lod_Chart.prototype.filter_qtl_results = function() { - var i, len, ref, result, results, this_chr; - this.these_results = []; - this_chr = 100; - ref = this.qtl_results; - results = []; - for (i = 0, len = ref.length; i < len; i++) { - result = ref[i]; - if (result.chr === "X") { - this_chr = this.max_chr; - } else { - this_chr = result.chr; - } - if (this_chr > parseInt(this.chr[0])) { - break; - } - if (parseInt(this_chr) === parseInt(this.chr[0])) { - results.push(this.these_results.push(result)); - } else { - results.push(void 0); - } - } - return results; - }; - - Chr_Lod_Chart.prototype.get_qtl_count = function() { - var high_qtl_count, i, len, ref, result; - high_qtl_count = 0; - ref = this.these_results; - for (i = 0, len = ref.length; i < len; i++) { - result = ref[i]; - if (result.lod_score > 1) { - high_qtl_count += 1; - } - } - console.log("high_qtl_count:", high_qtl_count); - return this.y_axis_filter = 2; - }; - - Chr_Lod_Chart.prototype.create_coordinates = function() { - var i, len, ref, result, results; - ref = this.these_results; - console.log("THESE_RESULTS:", ref) - results = []; - for (i = 0, len = ref.length; i < len; i++) { - result = ref[i]; - this.x_coords.push(parseFloat(result.Mb)); - if (js_data.result_score_type == "LOD") { - this.y_coords.push(result.lod_score); - } - else { - console.log("LRS VALUE:", result['lrs_value']) - this.y_coords.push(result['lrs_value']); - } - results.push(this.marker_names.push(result.name)); - } - return results; - }; - - Chr_Lod_Chart.prototype.create_svg = function() { - var svg; - svg = d3.select("#topchart").append("svg").attr("class", "chr_manhattan_plot").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer).append("g"); - return svg; - }; - - Chr_Lod_Chart.prototype.create_scales = function() { - if (this.mappingScale == "morgan") { - max_pos = 0 - for (i = 0, len = this.these_results.length; i < len; i++) { - marker = this.these_results[i] - if (parseFloat(marker['Mb']) > max_pos){ - max_pos = parseFloat(marker.Mb) - } - } - this.x_scale = d3.scale.linear().domain([0, max_pos]).range([this.x_buffer, this.plot_width]); - } - else { - this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]); - } - return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]); - }; - - Chr_Lod_Chart.prototype.get_lod_threshold = function() { - if (this.y_max / 2 > 2) { - return this.y_max / 2; - } else { - return 2; - } - }; - - Chr_Lod_Chart.prototype.create_graph = function() { - this.add_border(); - this.add_x_axis(); - this.add_y_axis(); - this.add_title(); - this.add_back_button(); - if (this.manhattanPlot) { - return this.add_plot_points(); - } else { - return this.add_path(); - } - }; - - Chr_Lod_Chart.prototype.add_border = function() { - var border_coords; - border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]]; - return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", (function(_this) { - return function(d) { - return d[0]; - }; - })(this)).attr("y2", (function(_this) { - return function(d) { - return d[1]; - }; - })(this)).attr("x1", (function(_this) { - return function(d) { - return d[2]; - }; - })(this)).attr("x2", (function(_this) { - return function(d) { - return d[3]; - }; - })(this)).style("stroke", "#000"); - }; - - Chr_Lod_Chart.prototype.add_x_axis = function() { - this.xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").ticks(20); - this.xAxis.tickFormat((function(_this) { - return function(d) { - d3.format("d"); - return d; - }; - })(this)); - return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(this.xAxis).selectAll("text").attr("text-anchor", "right").attr("font-size", "12px").attr("dx", "-1.6em").attr("transform", (function(_this) { - return function(d) { - return "translate(-12,0) rotate(-90)"; - }; - })(this)); - }; - - Chr_Lod_Chart.prototype.add_y_axis = function() { - this.yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); - return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(this.yAxis); - }; - - Chr_Lod_Chart.prototype.add_title = function() { - return this.svg.append("text").attr("class", "title").text("Chr " + this.chr[0]).attr("x", (function(_this) { - return function(d) { - return (_this.plot_width + _this.x_buffer) / 2; - }; - })(this)).attr("y", this.y_buffer + 20).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "black"); - }; - - Chr_Lod_Chart.prototype.add_back_button = function() { - return $("#return_to_full_view").show().click((function(_this) { - return function() { - return _this.return_to_full_view(); - }; - })(this)); - }; - - Chr_Lod_Chart.prototype.add_path = function() { - var line_function, line_graph; - line_function = d3.svg.line().x((function(_this) { - return function(d) { - return _this.x_scale(d[0]); - }; - })(this)).y((function(_this) { - return function(d) { - return _this.y_scale(d[1]); - }; - })(this)).interpolate("linear"); - return line_graph = this.svg.append("path").attr("d", line_function(this.plot_coordinates)).attr("stroke", "blue").attr("stroke-width", 1).attr("fill", "none"); - }; - - Chr_Lod_Chart.prototype.add_plot_points = function() { - return this.plot_point = this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", (function(_this) { - return function(d) { - return _this.x_scale(d[0]); - }; - })(this)).attr("cy", (function(_this) { - return function(d) { - return _this.y_scale(d[1]); - }; - })(this)).attr("r", (function(_this) { - return function(d) { - return 2; - }; - })(this)).attr("fill", (function(_this) { - return function(d) { - return "black"; - }; - })(this)).attr("stroke", "black").attr("stroke-width", "1").attr("id", (function(_this) { - return function(d) { - return "point_" + String(d[2]); - }; - })(this)).classed("circle", true).on("mouseover", (function(_this) { - return function(d) { - var this_id; - console.log("d3.event is:", d3.event); - console.log("d is:", d); - this_id = "point_" + String(d[2]); - return d3.select("#" + this_id).classed("d3_highlight", true).attr("r", 5).attr("stroke", "none").attr("fill", "blue").call(_this.show_marker_in_table(d)); - }; - })(this)).on("mouseout", (function(_this) { - return function(d) { - var this_id; - this_id = "point_" + String(d[2]); - return d3.select("#" + this_id).classed("d3_highlight", false).attr("r", function(d) { - return 2; - }).attr("fill", function(d) { - return "black"; - }).attr("stroke", "black").attr("stroke-width", "1"); - }; - })(this)).append("svg:title").text((function(_this) { - return function(d) { - return d[2]; - }; - })(this)); - }; - - Chr_Lod_Chart.prototype.return_to_full_view = function() { - $("#return_to_full_view").hide(); - $('#topchart').remove(); - $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); - return create_lod_chart(); - }; - - Chr_Lod_Chart.prototype.show_marker_in_table = function(marker_info) { - var marker_name; - console.log("in show_marker_in_table"); - - /* Searches for the select marker in the results table below */ - if (marker_info) { - marker_name = marker_info[2]; - return $("#qtl_results_filter").find("input:first").val(marker_name).change(); - } - }; - - return Chr_Lod_Chart; - -})(); |