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// 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;
})();
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