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// Generated by CoffeeScript 1.9.2
(function() {
var get_z_scores, redraw_prob_plot, root;
root = typeof exports !== "undefined" && exports !== null ? exports : this;
get_z_scores = function(n) {
var i, j, osm_uniform, ref, x;
osm_uniform = new Array(n);
osm_uniform[n - 1] = Math.pow(0.5, 1.0 / n);
osm_uniform[0] = 1 - osm_uniform[n - 1];
for (i = j = 1, ref = n - 2; 1 <= ref ? j <= ref : j >= ref; i = 1 <= ref ? ++j : --j) {
osm_uniform[i] = (i + 1 - 0.3175) / (n + 0.365);
}
return (function() {
var k, len, results;
results = [];
for (k = 0, len = osm_uniform.length; k < len; k++) {
x = osm_uniform[k];
results.push(jStat.normal.inv(x, 0, 1));
}
return results;
})();
};
redraw_prob_plot = function(samples, sample_group) {
var container, h, margin, totalh, totalw, w;
h = 600;
w = 500;
margin = {
left: 60,
top: 40,
right: 40,
bottom: 40,
inner: 5
};
totalh = h + margin.top + margin.bottom;
totalw = w + margin.left + margin.right;
container = $("#prob_plot_container");
container.width(totalw);
container.height(totalh);
return nv.addGraph((function(_this) {
return function() {
var W, all_samples, chart, data, intercept, make_data, names, pvalue, pvalue_str, slope, sorted_names, sorted_values, sw_result, test_str, x, z_scores;
chart = nv.models.scatterChart().width(w).height(h).showLegend(true).color(d3.scale.category10().range());
chart.pointRange([50, 50]);
chart.legend.updateState(false);
chart.xAxis.axisLabel("Expected Z score").axisLabelDistance(20).tickFormat(d3.format('.02f'));
chart.tooltipContent(function(obj) {
return '<b style="font-size: 20px">' + obj.point.name + '</b>';
});
all_samples = samples[sample_group];
names = (function() {
var j, len, ref, results;
ref = _.keys(all_samples);
results = [];
for (j = 0, len = ref.length; j < len; j++) {
x = ref[j];
if (all_samples[x] !== null) {
results.push(x);
}
}
return results;
})();
sorted_names = names.sort(function(x, y) {
return all_samples[x].value - all_samples[y].value;
});
max_decimals = 0
sorted_values = (function() {
var j, len, results;
results = [];
for (j = 0, len = sorted_names.length; j < len; j++) {
x = sorted_names[j];
results.push(all_samples[x].value);
if (all_samples[x].value.countDecimals() > max_decimals) {
max_decimals = all_samples[x].value.countDecimals()-1
}
}
return results;
})();
//ZS: 0.1 indicates buffer, increase to increase buffer
y_domain = [sorted_values[0] - (sorted_values.slice(-1)[0] - sorted_values[0])*0.1, sorted_values.slice(-1)[0] + (sorted_values.slice(-1)[0] - sorted_values[0])*0.1]
chart.yDomain(y_domain)
chart.yAxis.axisLabel("Trait value").axisLabelDistance(10).tickFormat(d3.format('.0'+max_decimals.toString()+'f'));
sw_result = ShapiroWilkW(sorted_values);
W = sw_result.w.toFixed(3);
pvalue = sw_result.p.toFixed(3);
pvalue_str = pvalue > 0.05 ? pvalue.toString() : "<span style='color:red'>" + pvalue + "</span>";
test_str = "Shapiro-Wilk test statistic is " + W + " (p = " + pvalue_str + ")";
z_scores = get_z_scores(sorted_values.length);
//ZS: 0.1 indicates buffer, increase to increase buffer
x_domain = [z_scores[0] - (z_scores.slice(-1)[0] - z_scores[0])*0.1, z_scores.slice(-1)[0] + (z_scores.slice(-1)[0] - z_scores[0])*0.1]
chart.xDomain(x_domain)
slope = jStat.stdev(sorted_values);
intercept = jStat.mean(sorted_values);
make_data = function(group_name) {
var sample, value, z_score;
return {
key: js_data.sample_group_types[group_name],
slope: slope,
intercept: intercept,
values: (function() {
var j, len, ref, ref1, results;
ref = _.zip(get_z_scores(sorted_values.length), sorted_values, sorted_names);
results = [];
for (j = 0, len = ref.length; j < len; j++) {
ref1 = ref[j], z_score = ref1[0], value = ref1[1], sample = ref1[2];
if (sample in samples[group_name]) {
results.push({
x: z_score,
y: value,
name: sample
});
}
}
return results;
})()
};
};
data = [make_data('samples_primary'), make_data('samples_other')];
d3.select("#prob_plot_container svg").datum(data).call(chart);
if (js_data.trait_symbol != null) {
$("#prob_plot_title").html("<h3>" + js_data.trait_symbol + ": " + js_data.trait_id + "</h3>");
} else {
$("#prob_plot_title").html("<h3>" + js_data.trait_id + "</h3>");
}
$("#shapiro_wilk_text").html(test_str)
$("#prob_plot_container .nv-legendWrap").toggle(sample_group === "samples_all");
return chart;
};
})(this));
};
root.redraw_prob_plot_impl = redraw_prob_plot;
}).call(this);
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