From 28a128b242af78941b7511e8f84ca5d61a19997c Mon Sep 17 00:00:00 2001 From: Lei Yan Date: Wed, 23 Aug 2017 15:26:26 +0000 Subject: Update corr scatterplot --- wqflask/wqflask/correlation/corr_scatter_plot.py | 15 ++ .../new/javascript/draw_corr_scatterplot-2_sr.js | 133 ++++++++++++ wqflask/wqflask/templates/corr_scatterplot.html | 239 ++++++++++++++------- 3 files changed, 315 insertions(+), 72 deletions(-) create mode 100644 wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2_sr.js diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 6a92c501..a08cd759 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -67,9 +67,17 @@ class CorrScatterPlot(object): x = np.array(vals_1) y = np.array(vals_2) slope, intercept, r_value, p_value, std_err = stats.linregress(x, y) + + rx = stats.rankdata(x) + ry = stats.rankdata(y) + self.rdata = [] + self.rdata.append(rx.tolist()) + self.rdata.append(ry.tolist()) + srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress(rx, ry) self.js_data = dict( data = self.data, + rdata = self.rdata, indIDs = self.indIDs, trait_1 = self.trait_1.dataset.name + ": " + str(self.trait_1.name), trait_2 = self.trait_2.dataset.name + ": " + str(self.trait_2.name), @@ -78,10 +86,17 @@ class CorrScatterPlot(object): num_overlap = num_overlap, vals_1 = vals_1, vals_2 = vals_2, + slope = slope, intercept = intercept, r_value = r_value, p_value = p_value, + + srslope = srslope, + srintercept = srintercept, + srr_value = srr_value, + srp_value = srp_value, + width = width, height = height, circle_color = circle_color, diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2_sr.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2_sr.js new file mode 100644 index 00000000..08ddc825 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2_sr.js @@ -0,0 +1,133 @@ +var srchart; + +function srdrawg () { + // + srchart = nv.models.scatterChart(); + // + srchart.showLegend(false); + srchart.duration(300); + srchart.color(d3.scale.category10().range()); + srchart.pointRange([0, 400]); + srchart.pointDomain([0, 10]); + // + srchart.xAxis.axisLabel(js_data.trait_1); + srchart.xAxis.axisLabelDistance(11); + srchart.yAxis.axisLabel(js_data.trait_2); + srchart.yAxis.axisLabelDistance(11); + // + xmin = d3.min(js_data.rdata[0]); + xmax = d3.max(js_data.rdata[0]); + xrange = xmax - xmin; + ymin = d3.min(js_data.rdata[1]); + ymax = d3.max(js_data.rdata[1]); + yrange = ymax - ymin; + srchart.xDomain([xmin - xrange/10, xmax + xrange/10]); + srchart.yDomain([ymin - yrange/10, ymax + yrange/10]); + srchart.xAxis.tickFormat(d3.format(srcheckformat(xrange))); + srchart.yAxis.tickFormat(d3.format(srcheckformat(yrange))); + // + srchart.tooltip.contentGenerator(function (obj) { + // return '(' + obj.point.x + ', ' + obj.point.y + ')'; + return '' + obj.point.name + ''; + }); +} + +function srgetdata(size, shape) { + var data = []; + data.push({ + values: [], + slope: js_data.srslope, + intercept: js_data.srintercept + }); + for (j = 0; j < js_data.rdata[0].length; j++) { + data[0].values.push({ + x: js_data.rdata[0][j], + y: js_data.rdata[1][j], + name: js_data.indIDs[j], + size: size, + shape: shape + }); + } + return data; +} + +function srcheckformat(range) { + cell = range / 10.0; + if (cell >= 1) { + return ",r"; + } else { + cell = -Math.log(cell); + n = cell.toString().split(".")[0].length; + return ",.0" + n + "f"; + } +} + +function srchartupdate() { + // + var axisxcolor = $("#axisxcolor").val(); + $(".nvd3 .nv-axis.nv-x text").css("fill", axisxcolor); + // + var axisycolor = $("#axisycolor").val(); + $(".nvd3 .nv-axis.nv-y text").css("fill", axisycolor); + // + var axisxfont = $("#axisxfont").val(); + $(".nvd3 .nv-axis.nv-x text").css("font-size", axisxfont); + // + var axisyfont = $("#axisyfont").val(); + $(".nvd3 .nv-axis.nv-y text").css("font-size", axisyfont); + // + var domainxcolor = $("#domainxcolor").val(); + $(".nv-x .nv-axis g path.domain").css("stroke", domainxcolor); + // + var domainycolor = $("#domainycolor").val(); + $(".nv-y .nv-axis g path.domain").css("stroke", domainycolor); + // + var domainxwidth = $("#domainxwidth").val(); + $(".nv-x .nv-axis g path.domain").css("stroke-width", domainxwidth); + // + var domainywidth = $("#domainywidth").val(); + $(".nv-y .nv-axis g path.domain").css("stroke-width", domainywidth); + // + var clinecolor = $("#clinecolor").val(); + $("line.nv-regLine").css("stroke", clinecolor); + // + var clinewidth = $("#clinewidth").val(); + $("line.nv-regLine").css("stroke-width", clinewidth); +} + +function srchartupdatewh() { + // + var width = $("#srwidth").val(); + $("#srscatterplot2 svg").css("width", width); + // + var height = $("#srheight").val(); + $("#srscatterplot2 svg").css("height", height); + // + window.dispatchEvent(new Event('resize')); +} + +function srchartupdatedata() { + // + var size = $("#srmarksize").val(); + var shape = $("#srmarkshape").val(); + // + d3.select('#srscatterplot2 svg').datum(nv.log(srgetdata(size, shape))).call(srchart); + nv.utils.windowResize(srchart.update); +} + +srdrawg(); +srchartupdate(); +srchartupdatewh(); +srchartupdatedata(); + +$(".srchartupdate").change(function () { + srchartupdate(); +}); + +$(".srchartupdatewh").change(function () { + srchartupdatewh(); +}); + +$(".srchartupdatedata").change(function () { + srchartupdatedata(); +}); diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html index 47b83018..fc9925e7 100644 --- a/wqflask/wqflask/templates/corr_scatterplot.html +++ b/wqflask/wqflask/templates/corr_scatterplot.html @@ -17,12 +17,65 @@

Correlation Scatterplot

+
+ + {% if trait_1.dataset.type == "ProbeSet" %} +
+ X axis: + + {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " " + trait_1.dataset.name + ": " + trait_1.name|string}} + +
+
+ [{{trait_1.symbol}} on {{trait_1.location_repr}} Mb] + {{trait_1.description_display}} +
+ {% elif trait_1.dataset.type == "Publish" %} +
+ X axis: + + {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}} + +
+
+ PubMed: {{trait_1.pubmed_text}} + {{trait_1.description_display}} +
+ {% endif %} + +
+ + {% if trait_2.dataset.type == "ProbeSet" %} +
+ Y axis: + + {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " " + trait_2.dataset.name + ": " + trait_2.name|string}} + +
+
+ [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb] + {{trait_2.description_display}} +
+ {% elif trait_2.dataset.type == "Publish" %} +
+ Y axis: + + {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}} + +
+
+ PubMed: {{trait_2.pubmed_text}} + {{trait_2.description_display}} +
+ {% endif %} + +
+ +
+ - - - @@ -38,6 +91,44 @@ + + + + + + + + + + + + + + + + + + + +
Width pxAxis X Color Correlation Line Color
Axis Y ColorAxis Y Font pxDomain Y ColorDomain Y Width pxCorrelation Line Width px
+ +
+ + + +
+
+ +
+ + + + + + - - - - - - - - - - - - - - - - - - - + + + +
Width pxMark Size Height pxAxis Y ColorAxis Y Font pxDomain Y ColorDomain Y Width pxCorrelation Line Width pxMark Shape + + + + + + + + + + +
StatisticValue
Number {{jsdata.num_overlap}}
Slope {{'%0.3f' % jsdata.slope}}
Intercept {{'%0.3f' % jsdata.intercept}}
r value {{'%0.3f' % jsdata.r_value}}
P value {{'%0.3e' % jsdata.p_value}}
- {% if trait_2.dataset.type == "ProbeSet" %} - -
- [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb] - {{trait_2.description_display}} -
- {% elif trait_2.dataset.type == "Publish" %} - -
- PubMed: {{trait_2.pubmed_text}} - {{trait_2.description_display}} -
- {% endif %} + + +
+ +
+ + + + + + + + + + + + + + + + + + +
Width pxMark Size + +
Height pxMark Shape + +
+ +
+

@@ -159,13 +247,19 @@
Number {{jsdata.num_overlap}}
Slope {{'%0.3f' % jsdata.slope}}
Intercept {{'%0.3f' % jsdata.intercept}}
R value {{'%0.3f' % jsdata.r_value}}
P value {{'%0.3e' % jsdata.p_value}}
Slope {{'%0.3f' % jsdata.srslope}}
Intercept {{'%0.3f' % jsdata.srintercept}}
r value {{'%0.3f' % jsdata.srr_value}}
P value {{'%0.3e' % jsdata.srp_value}}
+
+ +
+ + + {% endblock %} {% block js %} @@ -179,4 +273,5 @@ + {% endblock %} -- cgit v1.2.3