diff options
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/plotly_probability_plot.js | 246 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_statistics.html | 4 |
3 files changed, 248 insertions, 17 deletions
diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js new file mode 100644 index 00000000..49fd53b1 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js @@ -0,0 +1,246 @@ +// 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 = 600; + 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); + 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; + 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] + 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] + 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'), make_data('samples_all')]; + console.log("THE DATA IS:", data); + x_values = {} + y_values = {} + point_names = {} + for (i = 0; i < 3; i++){ + these_x_values = [] + these_y_values = [] + these_names = [] + for (j = 0; j < data[i].values.length; j++){ + these_x_values.push(data[i].values[j].x) + these_y_values.push(data[i].values[j].y) + these_names.push(data[i].values[j].name) + } + if (i == 0){ + x_values['samples_primary'] = these_x_values + y_values['samples_primary'] = these_y_values + point_names['samples_primary'] = these_names + } else if (i == 1) { + x_values['samples_other'] = these_x_values + y_values['samples_other'] = these_y_values + point_names['samples_other'] = these_names + } else { + x_values['samples_all'] = these_x_values + y_values['samples_all'] = these_y_values + point_names['samples_all'] = these_names + } + } + + intercept_line = {} + + if (sample_group == "samples_primary"){ + first_x = Math.floor(x_values['samples_primary'][0]) + first_x = first_x - first_x*0.1 + last_x = Math.ceil(x_values['samples_primary'][x_values['samples_primary'].length - 1]) + last_x = last_x + last_x*0.1 + first_value = data[0].intercept + data[0].slope * first_x + last_value = data[0].intercept + data[0].slope * last_x + intercept_line['samples_primary'] = [[first_x, last_x], [first_value, last_value]] + } else if (sample_group == "samples_other") { + first_x = Math.floor(x_values['samples_other'][0]) + first_x = first_x - first_x*0.1 + last_x = Math.ceil(x_values['samples_other'][x_values['samples_other'].length - 1]) + last_x = last_x + last_x*0.1 + first_value = data[1].intercept + data[1].slope * first_x + last_value = data[1].intercept + data[1].slope * last_x + intercept_line['samples_other'] = [[first_x, last_x], [first_value, last_value]] + } else { + first_x = Math.floor(x_values['samples_all'][0]) + first_x = first_x - first_x*0.1 + last_x = Math.ceil(x_values['samples_all'][x_values['samples_all'].length - 1]) + first_value = data[2].intercept + data[2].slope * first_x + last_x = last_x + last_x*0.1 + last_value = data[2].intercept + data[2].slope * last_x + intercept_line['samples_all'] = [[first_x, last_x], [first_value, last_value]] + } + + var layout = { + margin: { + l: 50, + r: 30, + t: 30, + b: 80 + }, + xaxis: { + range: [first_x, last_x], + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + }, + yaxis: { + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + } + } + + var primary_trace = { + x: x_values['samples_primary'], + y: y_values['samples_primary'], + mode: 'markers', + type: 'scatter', + name: js_data.sample_group_types['samples_primary'], + text: point_names['samples_primary'] + } + if ("samples_other" in js_data.sample_group_types) { + var other_trace = { + x: x_values['samples_other'], + y: y_values['samples_other'], + mode: 'markers', + type: 'scatter', + name: js_data.sample_group_types['samples_other'], + text: point_names['samples_other'] + } + } + + if (sample_group == "samples_primary"){ + var primary_intercept_trace = { + x: intercept_line['samples_primary'][0], + y: intercept_line['samples_primary'][1], + mode: 'lines', + type: 'scatter', + name: 'Intercept', + } + } else if (sample_group == "samples_other"){ + var other_intercept_trace = { + x: intercept_line['samples_other'][0], + y: intercept_line['samples_other'][1], + mode: 'lines', + type: 'scatter', + name: 'Intercept', + } + } else { + var all_intercept_trace = { + x: intercept_line['samples_all'][0], + y: intercept_line['samples_all'][1], + mode: 'lines', + type: 'scatter', + name: 'Intercept', + } + } + + if (sample_group == "samples_primary"){ + var data = [primary_trace, primary_intercept_trace] + } else if (sample_group == "samples_other"){ + var data = [other_trace, other_intercept_trace] + } else { + var data = [primary_trace, other_trace, all_intercept_trace] + } + + console.log("TRACE:", data) + Plotly.newPlot('prob_plot_div', data, layout) + }; + + root.redraw_prob_plot_impl = redraw_prob_plot; + +}).call(this); diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index dd4325e7..5d128b4a 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -133,34 +133,21 @@ <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script> <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script> <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script> - <script type="text/javascript" src="/static/new/js_external/saveSvgAsPng.js"></script> <script type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script> <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/bar_chart.js"></script> - <script type="text/javascript" src="/static/new/javascript/histogram.js"></script> - <script type="text/javascript" src="/static/new/javascript/box_plot.js"></script> - <script type="text/javascript" src="/static/new/javascript/scatterplot.js"></script> <script type="text/javascript" src="/static/new/javascript/scatter-matrix.js"></script> - <script type="text/javascript" src="/static/new/javascript/draw_probability_plot.js"></script> - <!--<script type="text/javascript" src="/static/new/javascript/plotly_probability_plot.js"></script>--> + <script type="text/javascript" src="/static/new/javascript/plotly_probability_plot.js"></script> <script type="text/javascript" src="/static/new/javascript/compare_traits_scatterplot.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.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> - <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/FileSaver.js/FileSaver.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script> <script type="text/javascript" charset="utf-8"> diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index aa95b083..09df3245 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -110,9 +110,7 @@ {% endif %} <div id="prob_plot_container"> - <div id="prob_plot_title"></div> - <svg></svg> - <!--<div id="prob_plot_div"></div>--> + <div id="prob_plot_div"></div> </div> <div id="shapiro_wilk_text"></div> <div> |