diff options
10 files changed, 137 insertions, 37 deletions
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 2cdd989f..6bc0ef77 100755 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -95,35 +95,24 @@ class CorrelationMatrix(object): #self.sample_data[this_trait.name].append('') self.sample_data.append(this_trait_vals) + self.lowest_overlap = 8 #ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning) + self.corr_results = [] - self.corr_results_for_pca = [] + self.pca_corr_results = [] for trait_db in self.trait_list: this_trait = trait_db[0] this_db = trait_db[1] this_db_samples = this_db.group.samplelist - - #for sample in this_db_samples: - # if sample not in self.samples: - # self.samples.append(sample) - this_sample_data = this_trait.data - print("this_sample_data", len(this_sample_data)) - - #for sample in this_sample_data: - # if sample not in self.all_sample_list: - # self.all_sample_list.append(sample) corr_result_row = [] + pca_corr_result_row = [] is_spearman = False #ZS: To determine if it's above or below the diagonal for target in self.trait_list: target_trait = target[0] target_db = target[1] target_samples = target_db.group.samplelist - - #if this_trait == target_trait and this_db == target_db: - # corr_result_row.append(1) - # continue target_sample_data = target_trait.data print("target_samples", len(target_samples)) @@ -139,19 +128,26 @@ class CorrelationMatrix(object): target_vals.append(target_sample_value) this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, target_vals) + + if num_overlap < self.lowest_overlap: + self.lowest_overlap = num_overlap if num_overlap == 0: corr_result_row.append([target_trait, 0, num_overlap]) + pca_corr_result_row.append(0) else: + pearson_r, pearson_p = scipy.stats.pearsonr(this_trait_vals, target_vals) if is_spearman == False: - sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, target_vals) + sample_r, sample_p = pearson_r, pearson_p if sample_r == 1: is_spearman = True else: sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals) corr_result_row.append([target_trait, sample_r, num_overlap]) + pca_corr_result_row.append(pearson_r) self.corr_results.append(corr_result_row) + self.pca_corr_results.append(pca_corr_result_row) print("corr_results:", pf(self.corr_results)) @@ -159,8 +155,9 @@ class CorrelationMatrix(object): for sample in self.all_sample_list: groups.append(1) - #pca = self.calculate_pca(self.corr_results, range(len(self.traits))) + pca = self.calculate_pca(self.pca_corr_results, range(len(self.traits))) + self.loadings_array = self.process_loadings() self.js_data = dict(traits = [trait.name for trait in self.traits], groups = groups, @@ -211,8 +208,24 @@ class CorrelationMatrix(object): print("eigen:", eigen) pca = stats.princomp(m, cor = "TRUE") print("pca:", pca) - print("loadings:", pca.rx('loadings')) + self.loadings = pca.rx('loadings') + self.scores = pca.rx('scores') + self.scale = pca.rx('scale') print("scores:", pca.rx('scores')) print("scale:", pca.rx('scale')) - return pca
\ No newline at end of file + return pca + + def process_loadings(self): + loadings_array = [] + loadings_row = [] + print("before loop:", self.loadings[0]) + for i in range(len(self.trait_list)): + loadings_row = [] + for j in range(3): + position = i + len(self.trait_list)*j + loadings_row.append(self.loadings[0][position]) + loadings_array.append(loadings_row) + print("loadings:", loadings_array) + return loadings_array + diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index b33efc1f..dc7ebfcc 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -74,6 +74,7 @@ class MarkerRegression(object): self.significant = "" self.pair_scan = False # Initializing this since it is checked in views to determine which template to use self.score_type = "LRS" #ZS: LRS or LOD + self.mapping_scale = "megabase" self.dataset.group.get_markers() if self.mapping_method == "gemma": @@ -86,6 +87,7 @@ class MarkerRegression(object): results = self.run_rqtl_plink() elif self.mapping_method == "rqtl_geno": self.score_type = "LOD" + self.mapping_scale = "centimorgan" if start_vars['num_perm'] == "": self.num_perm = 0 else: @@ -136,6 +138,7 @@ class MarkerRegression(object): data_set = self.dataset.name, maf = self.maf, manhattan_plot = self.manhattan_plot, + mapping_scale = self.mapping_scale, qtl_results = self.qtl_results, ) @@ -191,6 +194,7 @@ class MarkerRegression(object): data_set = self.dataset.name, maf = self.maf, manhattan_plot = self.manhattan_plot, + mapping_scale = self.mapping_scale, chromosomes = chromosome_mb_lengths, qtl_results = self.qtl_results, ) diff --git a/wqflask/wqflask/static/new/css/corr_matrix.css b/wqflask/wqflask/static/new/css/corr_matrix.css index f4838f77..495ca28c 100755 --- a/wqflask/wqflask/static/new/css/corr_matrix.css +++ b/wqflask/wqflask/static/new/css/corr_matrix.css @@ -10,3 +10,21 @@ width: 100px; float: left; } + +.chart { + +} + +.main text { + font: 10px sans-serif; +} + +.axis line, .axis path { + shape-rendering: crispEdges; + stroke: black; + fill: none; +} + +circle { + fill: steelblue; +} diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js index 616a89f6..60878978 100644 --- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js +++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js @@ -2,11 +2,12 @@ var Chr_Lod_Chart; Chr_Lod_Chart = (function() { - function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot) { + 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); @@ -65,8 +66,6 @@ Chr_Lod_Chart = (function() { } else { this_chr = result.chr; } - console.log("this_chr is:", this_chr); - console.log("@chr[0] is:", parseInt(this.chr[0])); if (this_chr > parseInt(this.chr[0])) { break; } @@ -120,7 +119,19 @@ Chr_Lod_Chart = (function() { }; Chr_Lod_Chart.prototype.create_scales = function() { - this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]); + if (this.mappingScale == "centimorgan") { + 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]); }; diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.js b/wqflask/wqflask/static/new/javascript/create_lodchart.js index b8fcf1f8..c756d842 100644 --- a/wqflask/wqflask/static/new/javascript/create_lodchart.js +++ b/wqflask/wqflask/static/new/javascript/create_lodchart.js @@ -16,8 +16,8 @@ halfh = h + margin.top + margin.bottom; totalh = halfh * 2; totalw = w + margin.left + margin.right; - //console.log("js_data:", js_data); - mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").manhattanPlot(js_data.manhattan_plot); + console.log("js_data:", js_data); + mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").mappingScale(js_data.mapping_scale).manhattanPlot(js_data.manhattan_plot); data = js_data.json_data; d3.select("div#topchart").datum(data).call(mychart); chrrect = mychart.chrSelect(); diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js index d0d39fe6..014bf59b 100644 --- a/wqflask/wqflask/static/new/javascript/lod_chart.js +++ b/wqflask/wqflask/static/new/javascript/lod_chart.js @@ -2,7 +2,7 @@ var lodchart; lodchart = function() { - var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks; + var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, mappingScale, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks; width = 800; height = 500; margin = { @@ -97,7 +97,7 @@ lodchart = function() { additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks); } reorgLodData(data, lodvarname); - data = chrscales(data, width, chrGap, margin.left, pad4heatmap); + data = chrscales(data, width, chrGap, margin.left, pad4heatmap, mappingScale); xscale = data.xscale; chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) { return "chrrect" + d[0]; @@ -133,7 +133,7 @@ lodchart = function() { var chr_plot; $('#topchart').remove(); $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); - return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot); + return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot, mappingScale); }; rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; yaxis = g.append("g").attr("class", "y axis"); @@ -305,6 +305,13 @@ lodchart = function() { manhattanPlot = value; return chart; }; + chart.mappingScale = function(value) { + if (!arguments.length) { + return mappingScale; + } + mappingScale = value; + return chart; + }; chart.ylim = function(value) { if (!arguments.length) { return ylim; diff --git a/wqflask/wqflask/static/new/javascript/panelutil.js b/wqflask/wqflask/static/new/javascript/panelutil.js index 113512b4..5a931f7d 100644 --- a/wqflask/wqflask/static/new/javascript/panelutil.js +++ b/wqflask/wqflask/static/new/javascript/panelutil.js @@ -105,7 +105,7 @@ reorgLodData = function(data, lodvarname) { return data; }; -chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) { +chrscales = function(data, width, chrGap, leftMargin, pad4heatmap, mappingScale) { var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1; chrStart = []; chrEnd = []; @@ -156,7 +156,15 @@ chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) { w = Math.round((width - chrGap * (data.chrnames.length - pad4heatmap)) / totalChrLength * chrLength[i]); data.chrEnd.push(cur + w); cur = data.chrEnd[i] + chrGap; - data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]); + + if (mappingScale == "centimorgan") { + max_pos = d3.max(data.posByChr[chr[0]]) + console.log("max_pos:", max_pos) + data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], max_pos]).range([data.chrStart[i], data.chrEnd[i]]); + } + else { + data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]); + } } return data; }; diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index c822b8bc..593c7bea 100755 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -12,7 +12,9 @@ {{ header("Correlation Matrix") }} - +{% if lowest_overlap < 8 %} +<div style="margin: 20px;" >Caution: This matrix of correlations contains some cells with small sample sizes of fewer than 8.</div> +{% endif %} <table class="matrix" border="1" cellpadding="5" cellspacing="1" style="margin: 20px;" width="80%"> <tbody> @@ -42,18 +44,48 @@ </tbody> </table> +<br> + +<div id="loadings_plot"></div> + +<table class="table table-hover table-striped" border="1" id='trait_table' style="margin: 20px;" width="40%"> + <thead> + <tr> + <th></th> + <th align="right" >Factor 1</th> + <th align="right" >Factor 2</th> + <th align="right" >Factor 2</th> <!-- -<div class="container"> - <div id="chart"></div> -</div> + {% for row in loadings_array %} + <th>Factor {{ loop.index }}</th> + {% endfor %} --> + </tr> + </thead> + <tbody> + {% for row in loadings_array %} + {% set row_counter = loop.index-1 %} + <tr> + <td> + <a href="{{ url_for('show_trait_page', trait_id = traits[loop.index-1].name, dataset = traits[loop.index-1].dataset.name) }}"> + {{ traits[loop.index-1].name }} + </a> + </td> + {% for column in row %} + <td><span style="float: right;">{{ '%0.3f' % loadings_array[row_counter][loop.index-1]|float }}</span></td> + {% endfor %} + </tr> + {% endfor %} + + </tbody> +</table> {% endblock %} {% block js %} <script> - js_data = {{ js_data | safe }} + loadings = {{ loadings_array | safe }} </script> <script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script> @@ -65,7 +97,6 @@ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> <script type="text/javascript" src="/static/new/javascript/panelutil.js"></script> <script language="javascript" type="text/javascript" src="/static/new/js_external/chroma.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/corr_matrix.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/create_corr_matrix.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/loadings_plot.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html index 2d0b6256..ad117337 100755 --- a/wqflask/wqflask/templates/marker_regression.html +++ b/wqflask/wqflask/templates/marker_regression.html @@ -36,7 +36,11 @@ <th>Index</th> <th>{{ score_type }}</th> <th>Chr</th> + {% if mapping_scale == "centimorgan" %} + <th>cM</th> + {% else %} <th>Mb</th> + {% endif %} <th>Locus</th> </tr> </thead> diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index f29b907d..e304be1c 100755 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -15,6 +15,7 @@ <input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}"> + <!-- Need to customize text more for other types of searches --> <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a> to find all records that match {% for word in search_terms %} @@ -49,6 +50,8 @@ <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ..."> <br /> <br /> +<!-- + Removing this until more options are added and work correctly {% if dataset.type == 'ProbeSet' %} <button class="btn btn-default" id="open_options">Open Extra Options</button> <br /> @@ -59,6 +62,7 @@ </div> <br /> <br /> +--> {% endif %} <div id="table_container"> <table class="table table-hover table-striped" id='trait_table' {% if dataset.type == 'Geno' %}width="400px"{% endif %} style="float: left;"> |