'
+ ## yay python 2.7
+ ro = fileinput.input(output_file, inplace=True, backup=".bak")
+ for roline in ro:
+ print(roline.replace(to_find, to_replace), end='')
+ ro.close()
+
+ return
+
+
+if __name__ == "__main__":
+ parser = ArgumentParser(
+ prog="csOverview",
+ description="Generate an overview plot of crossSample results.")
+
+ parser.add_argument(
+ '-i',
+ dest="input_file",
+ required=True,
+ help="File location for the summary statistics from CrossSample.")
+
+ parser.add_argument(
+ '-I',
+ dest="input_mfi",
+ required=True,
+ help="File location for the MFI summary statistics from CrossSample.")
+
+ parser.add_argument(
+ '-s',
+ dest="cs_outputs",
+ required=True,
+ action='append',
+ help="File location for the CrossSample output files.")
+
+ parser.add_argument(
+ '-o',
+ dest="output_file",
+ required=True,
+ help="File location for the HTML output file.")
+
+ parser.add_argument(
+ '-m',
+ dest="mfi",
+ required=True,
+ help="File location for the MFI from FLOCK.")
+
+ parser.add_argument(
+ '-d',
+ dest="output_directory",
+ required=True,
+ help="Directory location for the html supporting files.")
+
+ parser.add_argument(
+ '-t',
+ dest="tool_directory",
+ required=True,
+ help="Location of the Tool Directory.")
+
+ args = parser.parse_args()
+
+ cs_files = [f for f in args.cs_outputs]
+ cs_overview(args.input_file, args.input_mfi, args.mfi, args.output_file, args.output_directory, args.tool_directory, cs_files)
+ sys.exit(0)
diff -r 000000000000 -r 8c17aa8032c2 cs_overview/crossSampleOverview.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cs_overview/crossSampleOverview.xml Mon Feb 27 12:48:54 2017 -0500
@@ -0,0 +1,136 @@
+
+ of the CrossSample analysis
+
+ jinja2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 8c17aa8032c2 cs_overview/static/flowtools/css/parallelCoordinates.css
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cs_overview/static/flowtools/css/parallelCoordinates.css Mon Feb 27 12:48:54 2017 -0500
@@ -0,0 +1,170 @@
+/*Chart*/
+.chartDiv {
+ margin-top: 10px;
+ margin-bottom: 10px;
+ margin-left: 10px;
+ margin-right: 10px;
+ background-color: #ffffff;
+}
+/*This for stacked / bar plot*/
+.optionButtons{
+ padding-bottom: 8px;
+}
+.igbtn {
+ border-radius: 4px;
+ color: white;
+ background-color: #0E3163;
+ border:1px;
+ font-size: 14px;
+ font-weight: bold;
+ border-color: #0E3163;
+ padding: 6px 12px;
+ background: -webkit-linear-gradient(#0E3163, #3e6db0);
+ background: -o-linear-gradient(#0E3163, #3e6db0);
+ background: -moz-linear-gradient(#0E3163, #3e6db0);
+ background: linear-gradient(#0E3163, #3e6db0);
+}
+ #togglePlot {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+ height: 60px;
+ width: 90px;
+ padding: 4px 8px 8px 4px;
+}
+/*DataTables config*/
+div.dt-buttons {
+ float: right;
+}
+th {
+ background-color:#3965A4;
+ color:#fff;
+ border-radius: 2px;
+ padding:6px 12px;
+ font-size:14px;
+ text-align: center;
+}
+.igtable th {
+ background: -webkit-linear-gradient(#0E3163, #3e6db0);
+ background: -o-linear-gradient(#0E3163, #3e6db0);
+ background: -moz-linear-gradient(#0E3163, #3e6db0);
+ background: linear-gradient(#0E3163, #3e6db0)
+}
+body td {
+ max-width: 50px;
+ font-size: 14px;
+ overflow: hidden;
+ text-overflow: ellipsis;
+}
+.pctable td {
+ max-width: 100px;
+}
+.dtable td {
+ max-width: 50px;
+ word-break: break-all;
+ word-wrap: break-word;
+}
+.popt thead {
+ display:none;
+}
+.popt td {
+ max-width: 40px;
+ word-break: break-all;
+ word-wrap: break-word;
+}
+div.dataTables_wrapper {
+ width: 95%;
+ margin: 0 auto;
+}
+/*Opacity widget*/
+.widget {
+ margin-top: 4px;
+ padding: 4px 4px 8px 4px;
+ margin-bottom: 10px
+ height: 36px;
+ line-height: 12px;
+ font-size: 12px;
+ text-align: center;
+ // float: right;
+}
+/*This section for coordinates plot*/
+.table th {
+ text-align: center;
+ padding: 10px;
+}
+.table {
+ width:100%;
+ border:0px solid;
+ border-collapse:collapse;
+ text-align:center;
+ font-size: 14px;
+}
+svg {
+ font: 10px sans-serif;
+}
+.background path {
+ fill: none;
+ stroke: #F0F0F0;
+ shape-rendering: crispEdges;
+}
+.foreground path {
+ fill: none;
+ stroke-opacity: .8;
+}
+.brush .extent {
+ fill-opacity: .3;
+ stroke: #fff;
+ shape-rendering: crispEdges;
+}
+.axis line,
+.axis path {
+ fill: none;
+ stroke: #000;
+ stroke-width: 2;
+ shape-rendering: crispEdges;
+}
+.axis text {
+ text-shadow: 0 1px 0 #fff, 1px 0 0 #fff, 0 -1px 0 #fff, -1px 0 0 #fff;
+}
+.xlabel {
+ font-size: 14px;
+ fill: #808080;
+}
+.ylabel {
+ font-size: 16px;
+ fill: #808080;
+}
+/*This section for boxplots*/
+.box {
+ font: 10px sans-serif;
+}
+.box line,
+.box rect,
+.box circle {
+ fill: red;
+ stroke: #000;
+ stroke-width: 1px;
+}
+.box .center {
+ stroke-dasharray: 3,3;
+}
+.box .outlier {
+ fill: none;
+ stroke: #000;
+}
+.axisbp path,
+.axisbp line {
+ stroke-width: 1px;
+ fill:
+}
+.y.axisbp path {
+ stroke-width: 2;
+ stroke: #000;
+ fill: none;
+}
+.x.axisbp path {
+ fill: none;
+ stroke: #C8C8C8;
+ stroke-width: 0px;
+ shape-rendering: crispEdges;
+}
diff -r 000000000000 -r 8c17aa8032c2 cs_overview/static/flowtools/js/boxplots.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cs_overview/static/flowtools/js/boxplots.js Mon Feb 27 12:48:54 2017 -0500
@@ -0,0 +1,608 @@
+// Copyright (c) 2016 Northrop Grumman.
+// All rights reserved.
+
+var displayMarkerTable = function(plotconfig){
+ var nbm = plotconfig.mrkrNames.length + 1;
+ $(plotconfig.mtable).empty();
+ plotconfig.allMarkers.map(function(v) {
+ $(plotconfig.mtable).append('
'
+ + '| | '
+ + ''
+ + plotconfig.mrkrNames[v] + ' | '
+ + ' |
');
+ });
+ if (nbm > 5) {
+ $(plotconfig.mrkrSelectAll).prop('checked', false);
+ $(plotconfig.mrkrSelectAll).prop('disabled', true);
+ $('#markerWarning').show();
+ $(plotconfig.mrkrSelectj).each(function() {
+ var selectedMrkr = parseInt(this.value);
+ if (selectedMrkr > 4){
+ this.checked = false;
+ this.disabled = true;
+ } else {
+ this.checked = true;
+ }
+ });
+ }
+
+ $(plotconfig.mrkrSelectAll).click(function() {
+ var checkAll = $(plotconfig.mrkrSelectAll).prop('checked');
+ if (checkAll) {
+ $(plotconfig.mrkrSelectj).prop("checked", true);
+ } else {
+ $(plotconfig.mrkrSelectj).prop("checked", false);
+ }
+ updateCSplots(plotconfig);
+ });
+
+ $(plotconfig.mrkrSelectj).click(function() {
+ if (nbm < 6){
+ if ($(plotconfig.mrkrSelectj).length == $(plotconfig.mrkrSelectCheck).length) {
+ $(plotconfig.mrkrSelectAll).prop("checked",true);
+ } else {
+ $(plotconfig.mrkrSelectAll).prop("checked",false);
+ }
+ } else {
+ var nbSelected = 0;
+ $(plotconfig.mrkrSelectj).each(function() {
+ if (this.checked) {nbSelected++}
+ });
+ if (nbSelected < 5) {
+ $(plotconfig.mrkrSelectj).prop('disabled', false);
+ } else {
+ $(plotconfig.mrkrSelectj).each(function() {
+ if (!this.checked) {
+ this.disabled = true;
+ }
+ });
+ }
+ }
+ updateCSplots(plotconfig);
+ });
+};
+
+var updateBoxplot = function(plotconfig){
+ var margin = {top: 30, right: 10, bottom: 50, left: 60},
+ h = 0,
+ w = 0,
+ width = 0,
+ height = 0,
+ labels = false, // show the text labels beside individual boxplots?
+ mfi_option = false,
+ min = Infinity,
+ max = -Infinity,
+ checkLabels = $(plotconfig.displayvalues).prop("checked"),
+ checkMFI = $(plotconfig.displayMFI).prop("checked"),
+ dataToPlot = [],
+ tmp = [],
+ nbm = plotconfig.mrkrNames.length + 1,
+ maxRange = 0,
+ minRange = 0,
+ domainx = [],
+ domainx1 = [];
+
+ $(plotconfig.plotdivj).empty();
+ h = $(window).height() - 200;
+ $(plotconfig.plotdivj).height(h);
+ w = $(plotconfig.plotdivj).width();
+ width = w - margin.left - margin.right;
+ height = h - margin.top - margin.bottom;
+
+ var svg = d3.select(plotconfig.plotdivj).append("svg")
+ .attr("width", w)
+ .attr("height", h)
+ .attr("class", "box")
+ .append("g")
+ .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+ if (checkLabels) {
+ labels = true;
+ };
+ if (checkMFI) {
+ mfi_option = true;
+ };
+ /* Get the data in proper shape to feed to the boxplot function
+ want [Object, Object, ..., Object] where Object:
+ 'population': pop
+ 'Data' : [Object, Object, ..., Object] where Object:
+ 'Marker' : marker name
+ 'outliers' : outliers
+ */
+
+ if (plotconfig.view == 'p') {
+ plotconfig.selectedPopulations.forEach(function(p) {
+ tmpPlot = [];
+ plotconfig.selectedMarkers.forEach(function(m) {
+ var markernm = plotconfig.mrkrNames[m],
+ qtmp = [
+ +plotconfig.csdata.q1[markernm][p],
+ +plotconfig.csdata.q2[markernm][p],
+ +plotconfig.csdata.q3[markernm][p]
+ ],
+ wtmp = [
+ +plotconfig.csdata.lower[markernm][p],
+ +plotconfig.csdata.upper[markernm][p]
+ ];
+ tmp = [];
+ // Get min and max while we're here
+ plotconfig.csdata.outliers[markernm][p].forEach(function(outl) {
+ tmp.push(+outl);
+ if (+outl > max) {max = +outl};
+ if (+outl < min) {min = +outl};
+ });
+ if (+plotconfig.csdata.upper[markernm][p] > max) {
+ max = +plotconfig.csdata.upper[markernm][p];
+ };
+ if (+plotconfig.csdata.lower[markernm][p] < min) {
+ min = +plotconfig.csdata.lower[markernm][p];
+ };
+ tmpPlot.push({
+ marker: markernm,
+ outliers: tmp,
+ quartiles: qtmp,
+ whiskers: wtmp,
+ config: [m,p, nbm],
+ mfi: +plotconfig.csdata.mfi[markernm][p]
+ });
+ });
+ dataToPlot.push({population:p, popdata: tmpPlot});
+ });
+ } else {
+ plotconfig.selectedMarkers.forEach(function(m) {
+ var markernm = plotconfig.mrkrNames[m];
+ tmpPlot = [];
+ plotconfig.selectedPopulations.forEach(function(p) {
+ var qtmp = [
+ +plotconfig.csdata.q1[markernm][p],
+ +plotconfig.csdata.q2[markernm][p],
+ +plotconfig.csdata.q3[markernm][p]
+ ],
+ wtmp = [
+ +plotconfig.csdata.lower[markernm][p],
+ +plotconfig.csdata.upper[markernm][p]
+ ];
+ tmp = [];
+ // Get min and max while we're here
+ plotconfig.csdata.outliers[markernm][p].forEach(function(outl) {
+ tmp.push(+outl);
+ if (+outl > max) {max = +outl};
+ if (+outl < min) {min = +outl};
+ });
+ if (+plotconfig.csdata.upper[markernm][p] > max) {
+ max = +plotconfig.csdata.upper[markernm][p];
+ };
+ if (+plotconfig.csdata.lower[markernm][p] < min) {
+ min = +plotconfig.csdata.lower[markernm][p];
+ };
+ tmpPlot.push({
+ population:p,
+ outliers: tmp,
+ quartiles: qtmp,
+ whiskers: wtmp,
+ config: [m,p, nbm],
+ mfi: +plotconfig.csdata.mfi[markernm][p]
+ });
+ });
+ dataToPlot.push({marker: markernm, popdata: tmpPlot});
+ });
+ };
+ maxRange = max + 30;
+ minRange = min - 30;
+
+ if (plotconfig.view == 'p') {
+ domainx = plotconfig.selectedPopulations;
+ domainx1 = plotconfig.selectedMarkers.map(function(d){
+ return plotconfig.mrkrNames[d];
+ });
+ } else {
+ domainx1 = plotconfig.selectedPopulations;
+ domainx = plotconfig.selectedMarkers.map(function(d){
+ return plotconfig.mrkrNames[d];
+ });
+ }
+ // axes
+ var xScale = d3.scale.ordinal()
+ .domain(domainx)
+ .rangeRoundBands([0 , width], 0.2, 0.02);
+
+ var x1Scale = d3.scale.ordinal()
+ .domain(domainx1)
+ .rangeRoundBands([0, xScale.rangeBand()], 0.1);
+
+ var xAxis = d3.svg.axis()
+ .scale(xScale)
+ .orient("bottom");
+
+ // the y-axis
+ var yScale = d3.scale.linear()
+ .domain([minRange, maxRange])
+ .range([height + margin.top, 0 + margin.top]);
+
+ var yAxis = d3.svg.axis()
+ .scale(yScale)
+ .orient("left")
+ .tickFormat(d3.format("d"));
+
+ svg.append("g")
+ .attr("class", "x axisbp")
+ .attr("transform", "translate(0," + (height + margin.top) + ")")
+ .call(xAxis);
+
+ svg.append("g")
+ .attr("class", "y axisbp")
+ .call(yAxis)
+ .append("text")
+ .attr("class", "ylabel")
+ .attr("transform", "rotate(-90)")
+ .attr("y", 0 - margin.left)
+ .attr("x", 0 - (height / 2))
+ .attr("dy", "1em")
+ .style("text-anchor", "middle")
+ .text("MFI values");
+
+ var boxplot = d3.box()
+ .width(x1Scale.rangeBand())
+ .height(height + margin.top)
+ .domain([minRange, maxRange])
+ .showLabels(labels)
+ .showMFI(mfi_option);
+
+ if (plotconfig.view == 'p'){
+ var group = svg.selectAll(".groups")
+ .data(dataToPlot)
+ .enter().append("g")
+ .attr("class", "group")
+ .attr("transform", function(d) {
+ return "translate(" + xScale(d.population) + ",0)";
+ });
+
+ group.selectAll(".box")
+ .data(function(d) { return d.popdata; })
+ .enter().append("g")
+ .attr("transform", function(d) {return "translate(" + x1Scale(d.marker) + ",0)"; })
+ .call(boxplot);
+ } else {
+ var group = svg.selectAll(".groups")
+ .data(dataToPlot)
+ .enter().append("g")
+ .attr("class", "group")
+ .attr("transform", function(d) {
+ return "translate(" + xScale(d.marker) + ",0)";
+ });
+
+ group.selectAll(".box")
+ .data(function(d) { return d.popdata; })
+ .enter().append("g")
+ .attr("transform", function(d) { return "translate(" + x1Scale(d.population) + ",0)"; })
+ .call(boxplot);
+ }
+};
+
+(function() {
+ // Inspired by http://informationandvisualization.de/blog/box-plot
+ // Modified to fit our data structure.
+ d3.box = function() {
+ var width = 1,
+ height = 1,
+ duration = 0,
+ domain = null,
+ value = Number,
+ showLabels = true, // whether or not to show text labels
+ numBars = 4,
+ curBar = 1,
+ showMFI = true, // display MFI ?
+ tickFormat = null,
+ margin = {top: 30, right: 10, bottom: 50, left: 60};
+
+ // For each small multiple…
+ function box(g) {
+ g.each(function(data, i) {
+ var d = data.outliers.sort(d3.ascending),
+ g = d3.select(this),
+ n = d.length,
+ min = Infinity,
+ max = -Infinity;
+ if (n > 0){
+ min = d[0],
+ max = d[n - 1];
+ }
+ // Readjust min and max with upper and lower values
+ if (data.whiskers[0] < min) {min = data.whiskers[0]}
+ if (data.whiskers[1] > max) {max = data.whiskers[1]}
+ // Compute quartiles. Must return exactly 3 elements.
+ var quartileData = data.quartiles;
+ // Compute whiskers. Must return exactly 2 elements, or null.
+ var whiskerData = data.whiskers;
+ // Compute outliers. here all data in d is an outlier.
+ // We compute the outliers as indices, so that we can join across transitions!
+ var outlierIndices = d3.range(n);
+ var mfiData = data.mfi;
+ // this is the scale for ONE SET of values
+ // Compute the new x-scale.
+ var x1 = d3.scale.linear()
+ .domain(domain && domain.call(this, d, i) || [min, max])
+ .range([height , 0 + margin.top ]);
+ // Retrieve the old x-scale, if this is an update.
+ var x0 = this.__chart__ || d3.scale.linear()
+ .domain([0, Infinity])
+ .range(x1.range());
+
+ // Stash the new scale.
+ this.__chart__ = x1;
+// Note: the box, median, and box tick elements are fixed in number,
+// so we only have to handle enter and update. In contrast, the outliers
+// and other elements are variable, so we need to exit them! Variable
+// elements also fade in and out.
+ // Update center line: the vertical line spanning the whiskers.
+ var center = g.selectAll("line.center")
+ .data(whiskerData ? [whiskerData] : []);
+
+ //vertical line
+ center.enter().insert("line", "rect")
+ .attr("class", "center")
+ .attr("x1", width / 2)
+ .attr("y1", function(d) { return x0(d[0]); })
+ .attr("x2", width / 2)
+ .attr("y2", function(d) { return x0(d[1]); })
+ .style("opacity", 1e-6)
+ .style("stroke", function(d) { return color_palette[0][data.config[1]][3]; })
+ .transition()
+ .duration(duration)
+ .style("opacity", 1)
+ .attr("y1", function(d) { return x1(d[0]); })
+ .attr("y2", function(d) { return x1(d[1]); });
+
+ center.transition()
+ .duration(duration)
+ .style("opacity", 1)
+ .attr("y1", function(d) { return x1(d[0]); })
+ .attr("y2", function(d) { return x1(d[1]); });
+
+ center.exit().transition()
+ .duration(duration)
+ .style("opacity", 1e-6)
+ .attr("y1", function(d) { return x1(d[0]); })
+ .attr("y2", function(d) { return x1(d[1]); })
+ .remove();
+
+ // Update innerquartile box.
+ var box = g.selectAll("rect.box")
+ .data([quartileData]);
+
+ box.enter().append("rect")
+ .attr("class", "box")
+ .style("fill", function(d) {
+ var nbm = data.config[2],
+ pop = data.config[1],
+ mrkr = data.config[0];
+ var color = color_palette[0][pop][1] + (mrkr + 1 )/ nbm + ')';
+ return color; })
+ .style("stroke", function(d) { return color_palette[0][data.config[1]][3]; })
+ .attr("x", 0)
+ .attr("y", function(d) { return x0(d[2]); })
+ .attr("width", width)
+ .attr("height", function(d) { return x0(d[0]) - x0(d[2]); })
+ .transition()
+ .duration(duration)
+ .attr("y", function(d) { return x1(d[2]); })
+ .attr("height", function(d) { return x1(d[0]) - x1(d[2]); });
+
+ box.transition()
+ .duration(duration)
+ .attr("y", function(d) { return x1(d[2]); })
+ .attr("height", function(d) { return x1(d[0]) - x1(d[2]); });
+
+ // Update median line.
+ var medianLine = g.selectAll("line.median")
+ .data([quartileData[1]]);
+
+ medianLine.enter().append("line")
+ .attr("class", "median")
+ .attr("x1", 0)
+ .attr("y1", x0)
+ .attr("x2", width)
+ .attr("y2", x0)
+ .style("stroke", function(d) { return color_palette[0][data.config[1]][3]; })
+ .transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1);
+
+ medianLine.transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1);
+
+ // Update MFI line.
+ var MFILine = g.selectAll("line.mfi")
+ .data([mfiData]);
+ if (showMFI == true) {
+ MFILine.enter().append("line")
+ .attr("class", "mfi")
+ .style("stroke", function(d){ return color_palette[0][data.config[1]][2]; })
+ .attr("x1", 0)
+ .attr("y1", x0)
+ .attr("x2", width)
+ .attr("y2", x0)
+ .transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1);
+
+ MFILine.transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1);
+ }
+
+ // Update whiskers.
+ var whisker = g.selectAll("line.whisker")
+ .data(whiskerData || []);
+
+ whisker.enter().insert("line", "circle, text")
+ .attr("class", "whisker")
+ .attr("x1", 0)
+ .attr("y1", x0)
+ .attr("x2", 0 + width)
+ .attr("y2", x0)
+ .style("opacity", 1e-6)
+ .style("stroke", function(d) { return color_palette[0][data.config[1]][3]; })
+ .transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1)
+ .style("opacity", 1);
+
+ whisker.transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1)
+ .style("opacity", 1);
+
+ whisker.exit().transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1)
+ .style("opacity", 1e-6)
+ .remove();
+
+ // Update outliers.
+ var outlier = g.selectAll("circle.outlier")
+ .data(outlierIndices, Number);
+
+ outlier.enter().insert("circle", "text")
+ .attr("class", "outlier")
+ .attr("r", 3)
+ .attr("cx", function(d){
+ return Math.floor(Math.random() * width);
+ })
+ .attr("cy", function(i) { return x0(d[i]); })
+ .style("opacity", 1e-6)
+ .style("fill", function(d) {
+ var nbm = data.config[2],
+ pop = data.config[1],
+ mrkr = data.config[0];
+ var color = color_palette[0][pop][1] + (mrkr + 1 )/ nbm + ')';
+ return color; })
+ .style("stroke", function(d) { return color_palette[0][data.config[1]][3]; })
+ .transition()
+ .duration(duration)
+ .attr("cy", function(i) { return x1(d[i]); })
+ .style("opacity", 1);
+
+ outlier.transition()
+ .duration(duration)
+ .attr("cy", function(i) { return x1(d[i]); })
+ .style("opacity", 1);
+
+ outlier.exit().transition()
+ .duration(duration)
+ .attr("cy", function(i) { return x1(d[i]); })
+ .style("opacity", 1e-6)
+ .remove();
+
+ // Compute the tick format.
+ var format = tickFormat || x1.tickFormat(8);
+
+ // Update box ticks.
+ var boxTick = g.selectAll("text.box")
+ .data(quartileData);
+ if(showLabels == true) {
+ boxTick.enter().append("text")
+ .attr("class", "box")
+ .attr("dy", ".3em")
+ .attr("dx", function(d, i) { return i & 1 ? 6 : -6 })
+ .attr("x", function(d, i) { return i & 1 ? + width : 0 })
+ .attr("y", x0)
+ .attr("text-anchor", function(d, i) { return i & 1 ? "start" : "end"; })
+ .text(format)
+ .transition()
+ .duration(duration)
+ .attr("y", x1);
+ }
+
+ boxTick.transition()
+ .duration(duration)
+ .text(format)
+ .attr("y", x1);
+
+ // Update whisker ticks. These are handled separately from the box
+ // ticks because they may or may not exist, and we want don't want
+ // to join box ticks pre-transition with whisker ticks post-.
+ var whiskerTick = g.selectAll("text.whisker")
+ .data(whiskerData || []);
+ if(showLabels == true) {
+ whiskerTick.enter().append("text")
+ .attr("class", "whisker")
+ .attr("dy", ".3em")
+ .attr("dx", 6)
+ .attr("x", width)
+ .attr("y", x0)
+ .text(format)
+ .style("opacity", 1e-6)
+ .transition()
+ .duration(duration)
+ .attr("y", x1)
+ .style("opacity", 1);
+ }
+ whiskerTick.transition()
+ .duration(duration)
+ .text(format)
+ .attr("y", x1)
+ .style("opacity", 1);
+
+ whiskerTick.exit().transition()
+ .duration(duration)
+ .attr("y", x1)
+ .style("opacity", 1e-6)
+ .remove();
+ });
+ d3.timer.flush();
+ }
+
+ box.width = function(x) {
+ if (!arguments.length) return width;
+ width = x;
+ return box;
+ };
+ box.height = function(x) {
+ if (!arguments.length) return height;
+ height = x;
+ return box;
+ };
+ box.tickFormat = function(x) {
+ if (!arguments.length) return tickFormat;
+ tickFormat = x;
+ return box;
+ };
+ box.duration = function(x) {
+ if (!arguments.length) return duration;
+ duration = x;
+ return box;
+ };
+ box.domain = function(x) {
+ if (!arguments.length) return domain;
+ domain = x == null ? x : d3.functor(x);
+ return box;
+ };
+ box.value = function(x) {
+ if (!arguments.length) return value;
+ value = x;
+ return box;
+ };
+ box.showLabels = function(x) {
+ if (!arguments.length) return showLabels;
+ showLabels = x;
+ return box;
+ };
+ box.showMFI = function(x) {
+ if (!arguments.length) return showMFI;
+ showMFI = x;
+ return box;
+ };
+ return box;
+ };
+})();
diff -r 000000000000 -r 8c17aa8032c2 cs_overview/static/flowtools/js/color_palette.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cs_overview/static/flowtools/js/color_palette.js Mon Feb 27 12:48:54 2017 -0500
@@ -0,0 +1,226 @@
+// Copyright (c) 2016 Northrop Grumman.
+// All rights reserved.
+
+/* Palettes for graphics.
+* 0 -> Liz's palette (original ImmPort color scheme for graphics)
+* 1 -> Cris's palette (diverging)
+* 2 -> Christmas (diverging)
+* 3 -> not Christmas (sequential color blind friendly)
+* 4 -> Rainbow (sequential)
+* arrays are color HEX, color RGB (for transparency effect), contrasting color, darker shade for borders
+*/
+var color_palette = [[
+ ['#000000','rgba(0,0,0,','rgba(52,17,81,1)','#111111'],
+ ['#FF0000','rgba(255,0,0,','rgba(52,17,81,1)','#D21111'],
+ ['#FFFF00','rgba(255,255,0,','rgba(52,17,81,1)','#FFC900'],
+ ['#008000','rgba(0,128,0,','rgba(52,17,81,1)','#016D01'],
+ ['#0000FF','rgba(0,0,255,','rgba(255,0,0,1)','#2121A0'],
+ ['#FFA500','rgba(255,165,0,','rgba(52,17,81,1)','#DE991B'],
+ ['#8A2BE2','rgba(138,43,226,','rgba(52,17,81,1)','#6A0EBF'],
+ ['#808000','rgba(128,128,0,','rgba(52,17,81,1)','#66660A'],
+ ['#00FFFF','rgba(0,255,255,','rgba(52,17,81,1)','#1DCBCB'],
+ ['#FF00FF','rgba(255,0,255,','rgba(52,17,81,1)','#A009A0'],
+ ['#00FF00','rgba(0,255,0,','rgba(52,17,81,1)','#20AB20'],
+ ['#000080','rgba(0,0,128,','rgba(255,0,0,1)','#13135B'],
+ ['#F08080','rgba(240,128,128,','rgba(52,17,81,1)','#922626'],
+ ['#800080','rgba(128,0,128,','rgba(255,0,0,1)','#580B58'],
+ ['#F0E68C','rgba(240,230,140,','rgba(52,17,81,1)','#F0C08C'],
+ ['#8FBC8F','rgba(143,188,143,','rgba(52,17,81,1)','#668166'],
+ ['#2F4F4F','rgba(47,79,79,','rgba(52,17,81,1)','#0E3636'],
+ ['#008080','rgba(0,128,128,','rgba(52,17,81,1)','#095454'],
+ ['#9932CC','rgba(153,50,204,','rgba(52,17,81,1)','#78289F'],
+ ['#FF7F50','rgba(255,127,80,','rgba(52,17,81,1)','#B0431A'],
+ ['#FFD700','rgba(255,215,0,','rgba(52,17,81,1)','#FFB900'],
+ ['#008B8B','rgba(0,139,139,','rgba(52,17,81,1)','#097171'],
+ ['#800000','rgba(128,0,0,','rgba(255,0,0,1)','#500303'],
+ ['#5F9EA0','rgba(95,158,160,','rgba(52,17,81,1)','#366668'],
+ ['#FFC0CB','rgba(255,192,203,','rgba(52,17,81,1)','#FC869B'],
+ ['#545454','rgba(84,84,84,','rgba(255,0,0,1)','#342C2C'],
+ ['#7FFFD4','rgba(127,255,212,','rgba(255,0,0,1)','#8CCAB5'],
+ ['#ADD8E6','rgba(173,216,230,','rgba(52,17,81,1)','#77C6DF'],
+ ['#DB7093','rgba(219,112,147,','rgba(52,17,81,1)','#B24B6D'],
+ ['#CD853F','rgba(205,133,63,','rgba(52,17,81,1)','#BA6D22'],
+ ['#4169E1','rgba(65,105,225,','rgba(52,17,81,1)','#1840B8'],
+ ['#708090','rgba(112,128,144,','rgba(52,17,81,1)','#465A6D'],
+ ['#4682B4','rgba(70,130,180,','rgba(52,17,81,1)','#1F5785'],
+ ['#D8BFD8','rgba(216,191,216,','rgba(52,17,81,1)','#B679B6'],
+ ['#F5DEB3','rgba(245,222,179,','rgba(52,17,81,1)','#E9AB3F'],
+ ['#9ACD32','rgba(154,205,50,','rgba(52,17,81,1)','#6E971B'],
+ ['#BDB76B','rgba(189,183,107,','rgba(52,17,81,1)','#938E49'],
+ ['#8B008B','rgba(139,0,139,','rgba(255,0,0,1)','#590A59'],
+ ['#556B2F','rgba(85,107,47,','rgba(52,17,81,1)','#3A4D19'],
+ ['#00CED1','rgba(0,206,209,','rgba(52,17,81,1)','#1BA0A2'],
+ ['#FF1493','rgba(255,20,147,','rgba(52,17,81,1)','#A40F5F']
+],[
+ //cris
+ ['#000000','rgba(0,0,0,','rgba(52,17,81,1)','#111111'],
+ ['#5B1A48','rgba(91,26,72,','rgba(255,0,0,1)','#922B74'],
+ ['#1ED992','rgba(30,217,146,','rgba(52,17,81,1)','#108A5B'],
+ ['#FFE4FF','rgba(255,228,255,','rgba(52,17,81,1)','#FF9AFF'],
+ ['#3B2000','rgba(59,32,0,','rgba(255,0,0,1)','#8C4D02'],
+ ['#BDF765','rgba(189,247,101,','rgba(52,17,81,1)','#83b438'],
+ ['#C6DCFD','rgba(198,220,253,','rgba(52,17,81,1)','#70A9FE'],
+ ['#542788','rgba(84,39,136,','rgba(255,0,0,1)','#8055B2'],
+ ['#FB8072','rgba(251,128,114,','rgba(52,17,81,1)','#D55446'],
+ ['#F2E0B8','rgba(242,224,184,','rgba(52,17,81,1)','#F9C146'],
+ ['#0A684C','rgba(10,104,76,','rgba(52,17,81,1)','#27B88D'],
+ ['#FD8ADC','rgba(253,138,220,','rgba(52,17,81,1)','#CB3AA2'],
+ ['#CDFAFF','rgba(205,250,255,','rgba(52,17,81,1)','#66EDFC'],
+ ['#0C1657','rgba(12,22,87,','rgba(255,0,0,1)','#3243B6'],
+ ['#FFDE69','rgba(255,222,105,','rgba(52,17,81,1)','#CFAD34'],
+ ['#BEBADA','rgba(190,186,218,','rgba(52,17,81,1)','#6A5EBA'],
+ ['#8D182B','rgba(141,24,43,','rgba(52,17,81,1)','#5E0412'],
+ ['#FFFF00','rgba(255,255,0,','rgba(52,17,81,1)','#FFC900'],
+ ['#788D84','rgba(120,141,132,','rgba(52,17,81,1)','#496F5F'],
+ ['#A53DD5','rgba(165,61,213,','rgba(52,17,81,1)','#66178A'],
+ ['#5DF33F','rgba(93,243,63,','rgba(52,17,81,1)','#47A035'],
+ ['#C8C8C8','rgba(200,200,200,','rgba(52,17,81,1)','#878484'],
+ ['#9A1B7D','rgba(154,27,125,','rgba(52,17,81,1)','#D54BB5'],
+ ['#1068BD','rgba(16,104,189,','rgba(52,17,81,1)','#0C3156'],
+ ['#C7EAE5','rgba(199,234,229,','rgba(52,17,81,1)','#68B8AC'],
+ ['#8C510A','rgba(140,81,10,','rgba(52,17,81,1)','#653B07'],
+ ['#FFBD01','rgba(255,189,1,','rgba(52,17,81,1)','#CE9800'],
+ ['#DFFCC5','rgba(223,252,197,','rgba(52,17,81,1)','#99C670'],
+ ['#41C8C4','rgba(65,200,196,','rgba(52,17,81,1)','#24918E'],
+ ['#9685F5','rgba(150,133,245,','rgba(52,17,81,1)','#6257A1'],
+ ['#D8B365','rgba(216,179,101,','rgba(52,17,81,1)','#9F7E39'],
+ ['#00FFFF','rgba(0,255,255,','rgba(52,17,81,1)','#1DCBCB'],
+ ['#F1F1A2','rgba(241,241,162,','rgba(52,17,81,1)','#CECE54'],
+ ['#AFBFFD','rgba(175,191,253,','rgba(52,17,81,1)','#5E72BF'],
+ ['#FF0019','rgba(255,0,25,','rgba(52,17,81,1)','#970110'],
+ ['#8A598A','rgba(138,89,138,','rgba(52,17,81,1)','#602E60'],
+ ['#75B030','rgba(117,176,48,','rgba(52,17,81,1)','#3D690A'],
+ ['#0A5A83','rgba(10,90,131,','rgba(52,17,81,1)','#0F3447'],
+ ['#937B6A','rgba(147,123,106,','rgba(52,17,81,1)','#473121'],
+ ['#1540EC','rgba(21,64,236,','rgba(255,0,0,1)','#0C2589'],
+ ['#010101','rgba(1,1,1,','rgba(255,0,0,1)','#4A4242']
+],[
+ //christmas
+ ['#000000','rgba(0,0,0,','rgba(52,17,81,1)','#111111'],
+ ['#BD1A00','rgba(189,26,0,','rgba(52,17,81,1)','#7B1E0F'],
+ ['#FF8F68','rgba(255,143,104,','rgba(52,17,81,1)','#BC4F28'],
+ ['#FFFFBF','rgba(255,255,191,','rgba(52,17,81,1)','#EAEA72'],
+ ['#1A9850','rgba(26,152,80,','rgba(52,17,81,1)','#0F582F'],
+ ['#BDF765','rgba(189,247,101,','rgba(52,17,81,1)','#73B70C'],
+ ['#542788','rgba(84,39,136,','rgba(255,0,0,1)','#230941'],
+ ['#998EC3','rgba(153,142,195,','rgba(52,17,81,1)','#483884'],
+ ['#D8DAEB','rgba(216,218,235,','rgba(52,17,81,1)','#7581E9'],
+ ['#5A95B8','rgba(90,149,184,','rgba(52,17,81,1)','#154C6C'],
+ ['#01555E','rgba(1,85,94,','rgba(255,0,0,1)','#04272A'],
+ ['#FEE0B6','rgba(254,224,182,','rgba(52,17,81,1)','#C8954F'],
+ ['#F1A340','rgba(241,163,64,','rgba(52,17,81,1)','#BD7519'],
+ ['#B35806','rgba(179,88,6,','rgba(52,17,81,1)','#683303'],
+ ['#8D182B','rgba(141,24,43,','rgba(52,17,81,1)','#5B0B18'],
+ ['#EF8AB4','rgba(239,138,180,','rgba(52,17,81,1)','#E7337E'],
+ ['#C51B7D','rgba(197,27,125,','rgba(52,17,81,1)','#690840'],
+ ['#3B2000','rgba(59,32,0,','rgba(255,0,0,1)','#120A00'],
+ ['#8C510A','rgba(140,81,10,','rgba(52,17,81,1)','#442907'],
+ ['#D8B365','rgba(216,179,101,','rgba(52,17,81,1)','#816426'],
+ ['#C7EAE5','rgba(199,234,229,','rgba(52,17,81,1)','#54AB9F'],
+ ['#41B6C4','rgba(65,182,196,','rgba(52,17,81,1)','#167D89'],
+ ['#225EA8','rgba(34,94,168,','rgba(52,17,81,1)','#103B6F'],
+ ['#0C1657','rgba(12,22,87,','rgba(255,0,0,1)','#030933'],
+ ['#00FF00','rgba(0,255,0,','rgba(52,17,81,1)','#20AB20'],
+ ['#FF0000','rgba(255,0,0,','rgba(52,17,81,1)','#D21111'],
+ ['#AFAFAF','rgba(175,175,175,','rgba(52,17,81,1)','#818D8D'],
+ ['#FFFF00','rgba(255,255,0,','rgba(52,17,81,1)','#FFC900'],
+ ['#FF00DB','rgba(255,0,219,','rgba(52,17,81,1)','#A70C91'],
+ ['#0000FF','rgba(0,0,255,','rgba(255,0,0,1)','#2121A0'],
+ ['#00FFFF','rgba(0,255,255,','rgba(52,17,81,1)','#1DCBCB'],
+ ['#95E199','rgba(149,225,153,','rgba(52,17,81,1)','#369F3B'],
+ ['#A53DD5','rgba(165,61,213,','rgba(52,17,81,1)','#590480'],
+ ['#1A4A26','rgba(26,74,38,','rgba(255,0,0,1)','#08240F'],
+ ['#FCCDE5','rgba(252,205,229,','rgba(52,17,81,1)','#D082AA'],
+ ['#FDB462','rgba(255,222,105,','rgba(52,17,81,1)','#D77C15'],
+ ['#FFDE69','rgba(253,180,98,','rgba(52,17,81,1)','#E6B505'],
+ ['#80B1D3','rgba(128,177,211,','rgba(52,17,81,1)','#306E99'],
+ ['#737B1B','rgba(115,123,27,','rgba(52,17,81,1)','#424705'],
+ ['#BEBADA','rgba(190,186,218,','rgba(52,17,81,1)','#514984'],
+ ['#8DD3C7','rgba(141,211,199,','rgba(52,17,81,1)','#248D7B']
+],[
+// Not christmas
+ ['#000000','rgba(0,0,0,','rgba(52,17,81,1)','#111111'],
+ ['#781C81','rgba(120,28,129,','rgba(255,0,0,1)','#49074F'],
+ ['#61187E','rgba(97,24,126,','rgba(255,0,0,1)','#3B0251'],
+ ['#531B7F','rgba(83,27,127,','rgba(255,0,0,1)','#320356'],
+ ['#4A2384','rgba(74,35,132,','rgba(255,0,0,1)','#260656'],
+ ['#442E8A','rgba(68,46,138,','rgba(255,0,0,1)','#1E0A5C'],
+ ['#413B93','rgba(65,59,147,','rgba(255,0,0,1)','#18125E'],
+ ['#3F499D','rgba(63,73,157,','rgba(255,0,0,1)','#17206F'],
+ ['#3F58A8','rgba(63,88,168,','rgba(255,0,0,1)','#11276C'],
+ ['#4066B2','rgba(64,102,178,','rgba(255,0,0,1)','#16377B'],
+ ['#4273BB','rgba(66,115,187,','rgba(255,0,0,1)','#13438A'],
+ ['#447FC0','rgba(68,127,192,','rgba(52,17,81,1)','#164F8E'],
+ ['#488AC2','rgba(72,138,194,','rgba(52,17,81,1)','#195A92'],
+ ['#4C94BF','rgba(76,148,191,','rgba(52,17,81,1)','#1C6490'],
+ ['#519CB8','rgba(81,156,184,','rgba(52,17,81,1)','#1E6D8B'],
+ ['#57A3AE','rgba(87,163,174,','rgba(52,17,81,1)','#287985'],
+ ['#5EA9A2','rgba(94,169,162,','rgba(52,17,81,1)','#277A72'],
+ ['#65AE95','rgba(101,174,149,','rgba(52,17,81,1)','#28785D'],
+ ['#6DB388','rgba(109,179,136,','rgba(52,17,81,1)','#348252'],
+ ['#76B67D','rgba(118,182,125,','rgba(52,17,81,1)','#388340'],
+ ['#7FB972','rgba(127,185,114,','rgba(52,17,81,1)','#448635'],
+ ['#88BB69','rgba(136,187,105,','rgba(52,17,81,1)','#518730'],
+ ['#92BD60','rgba(146,189,96,','rgba(52,17,81,1)','#62902D'],
+ ['#9CBE59','rgba(156,190,89,','rgba(52,17,81,1)','#6D9028'],
+ ['#A7BE53','rgba(167,190,83,','rgba(52,17,81,1)','#70871D'],
+ ['#B1BE49','rgba(177,190,78,','rgba(52,17,81,1)','#7C8919'],
+ ['#BABC49','rgba(186,188,73,','rgba(52,17,81,1)','#87891B'],
+ ['#C3BA45','rgba(195,186,69,','rgba(52,17,81,1)','#928917'],
+ ['#CCB742','rgba(204,183,66,','rgba(52,17,81,1)','#AC9516'],
+ ['#D3B33F','rgba(211,179,63,','rgba(52,17,81,1)','#A78713'],
+ ['#DAAD3C','rgba(218,173,60,','rgba(52,17,81,1)','#AB7E0D'],
+ ['#DFA539','rgba(223,165,57,','rgba(52,17,81,1)','#B17609'],
+ ['#E39C37','rgba(227,156,55,','rgba(52,17,81,1)','#BB730D'],
+ ['#E59134','rgba(229,145,52,','rgba(52,17,81,1)','#B16006'],
+ ['#E78432','rgba(231,132,50,','rgba(52,17,81,1)','#B45404'],
+ ['#E7752F','rgba(231,117,47,','rgba(52,17,81,1)','#763703'],
+ ['#E6652D','rgba(230,101,45,','rgba(52,17,81,1)','#AD3906'],
+ ['#E4542A','rgba(228,84,42,','rgba(52,17,81,1)','#AE2A04'],
+ ['#E14326','rgba(225,67,38,','rgba(52,17,81,1)','#AD1E04'],
+ ['#DD3123','rgba(221,49,35,','rgba(52,17,81,1)','#A11105'],
+ ['#D92120','rgba(217,33,32,','rgba(52,17,81,1)','#8A0201']
+],[
+// Rainbow
+ ['#000000','rgba(0,0,0,','rgba(52,17,81,1)','#111111'],
+ ['#FF0000','rgba(255,0,0,','rgba(52,17,81,1)','#C30707'],
+ ['#FF2600','rgba(255,38,0,','rgba(52,17,81,1)','#BA250B'],
+ ['#FF4D00','rgba(255,77,0,','rgba(52,17,81,1)','#BD3A02'],
+ ['#FF7300','rgba(255,115,0,','rgba(52,17,81,1)','#C15B06'],
+ ['#FF9900','rgba(255,153,0,','rgba(52,17,81,1)','#BF7504'],
+ ['#FFBF00','rgba(255,191,0,','rgba(52,17,81,1)','#C49405'],
+ ['#FFE500','rgba(255,229,0,','rgba(52,17,81,1)','#BEAB01'],
+ ['#F2FF00','rgba(242,255,0,','rgba(52,17,81,1)','#B3BD03'],
+ ['#CCFF00','rgba(204,255,0,','rgba(52,17,81,1)','#93B607'],
+ ['#A6FF00','rgba(166,255,0,','rgba(52,17,81,1)','#7BBB05'],
+ ['#80FF00','rgba(128,255,0,','rgba(52,17,81,1)','#59AC05'],
+ ['#59FF00','rgba(89,255,0,','rgba(52,17,81,1)','#3DAD01'],
+ ['#33FF00','rgba(51,255,0,','rgba(52,17,81,1)','#24B001'],
+ ['#0DFF00','rgba(13,255,0,','rgba(52,17,81,1)','#0CAA03'],
+ ['#00FF1A','rgba(0,255,26,','rgba(52,17,81,1)','#03AC14'],
+ ['#00FF40','rgba(0,255,64,','rgba(52,17,81,1)','#02AB2C'],
+ ['#00FF66','rgba(0,255,102,','rgba(52,17,81,1)','#01AD46'],
+ ['#00FF8C','rgba(0,255,140,','rgba(52,17,81,1)','#06B466'],
+ ['#00FFB3','rgba(0,255,179,','rgba(52,17,81,1)','#01AB79'],
+ ['#00FFD9','rgba(0,255,217,','rgba(52,17,81,1)','#02B399'],
+ ['#00FFFF','rgba(0,255,255,','rgba(52,17,81,1)','#04AEAE'],
+ ['#00D9FF','rgba(0,217,255,','rgba(52,17,81,1)','#0496B0'],
+ ['#00B2FF','rgba(0,178,255,','rgba(52,17,81,1)','#0272A3'],
+ ['#008CFF','rgba(0,140,255,','rgba(255,0,0,1)','#00569D'],
+ ['#0068FF','rgba(0,102,255,','rgba(255,0,0,1)','#044AAE'],
+ ['#0040FF','rgba(0,64,255,','rgba(255,0,0,1)','#032894'],
+ ['#0019FF','rgba(0,25,255,','rgba(255,0,0,1)','#01109C'],
+ ['#0D00FF','rgba(13,0,255,','rgba(255,0,0,1)','#0B03A7'],
+ ['#3300FF','rgba(51,0,255,','rgba(255,0,0,1)','#2403A7'],
+ ['#5900FF','rgba(89,0,255,','rgba(255,0,0,1)','#3E04AA'],
+ ['#8000FF','rgba(128,0,255,','rgba(255,0,0,1)','#5302A4'],
+ ['#A600FF','rgba(166,0,255,','rgba(255,0,0,1)','#6F03A9'],
+ ['#CC00FF','rgba(204,0,255,','rgba(255,0,0,1)','#8A04AC'],
+ ['#F200FF','rgba(242,0,255,','rgba(52,17,81,1)','#9D03A5'],
+ ['#FF00E5','rgba(255,0,229,','rgba(52,17,81,1)','#B607A4'],
+ ['#FF00BF','rgba(255,0,191,','rgba(52,17,81,1)','#B40588'],
+ ['#FF0099','rgba(255,0,153,','rgba(52,17,81,1)','#B4016D'],
+ ['#FF0073','rgba(255,0,115,','rgba(52,17,81,1)','#A9024D'],
+ ['#FF004C','rgba(255,0,76,','rgba(52,17,81,1)','#A90335'],
+ ['#FF0026','rgba(255,0,38,','rgba(52,17,81,1)','#A6051D']
+]];
diff -r 000000000000 -r 8c17aa8032c2 cs_overview/static/flowtools/js/crossSamplePlots.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cs_overview/static/flowtools/js/crossSamplePlots.js Mon Feb 27 12:48:54 2017 -0500
@@ -0,0 +1,263 @@
+// Copyright (c) 2016 Northrop Grumman.
+// All rights reserved.
+var updateCSplots = function(plotconfig){
+ plotconfig.selectedPopulations = [];
+ $(plotconfig.popSelectj).each(function() {
+ if (this.checked) {
+ plotconfig.selectedPopulations.push(parseInt(this.value));
+ }
+ });
+ if (plotconfig.hasOwnProperty("mtable")) {
+ // Update selected markers?
+ plotconfig.selectedMarkers = [];
+ $(plotconfig.mrkrSelectj).each(function() {
+ if (this.checked) {
+ plotconfig.selectedMarkers.push(parseInt(this.value));
+ }
+ });
+ // update plot
+ updateBoxplot(plotconfig);
+ } else {
+ updatePlot(plotconfig);
+ }
+};
+
+var displayPopulationLegend = function(plotconfig) {
+ $(plotconfig.table).empty();
+ plotconfig.allPopulations.map(function(value,index) {
+ $(plotconfig.table).append('
| '
+ + ' | '
+ + newPopNames[value] + ' | |
');
+ });
+
+ $(plotconfig.popSelectAll).click(function() {
+ var checkAll = $(plotconfig.popSelectAll).prop('checked');
+ if (checkAll) {
+ $(plotconfig.popSelectj).prop("checked", true);
+ } else {
+ $(plotconfig.popSelectj).prop("checked", false);
+ }
+ updateCSplots(plotconfig);
+ });
+
+ $(plotconfig.popSelectj).click(function() {
+ if ($(plotconfig.popSelectj).length == $(plotconfig.popSelectCheck).length) {
+ $(plotconfig.popSelectAll).prop("checked",true);
+ } else {
+ $(plotconfig.popSelectAll).prop("checked",false);
+ }
+ updateCSplots(plotconfig);
+ });
+
+ $(plotconfig.popSelectj).each(function() {
+ var selectedpopn = parseInt(this.value);
+ if ($.inArray(selectedpopn,plotconfig.selectedPopulations) > -1) {
+ this.checked = true;
+ } else {
+ this.checked = false;
+ }
+ });
+};
+
+var displayToolbar = function(plotconfig){
+ $(plotconfig.displaybutton).on("click",function() {
+ $(plotconfig.popSelectj).prop("checked", true);
+ $(plotconfig.popSelectAll).prop("checked", true);
+ if (plotconfig.hasOwnProperty("mtable")){
+ $(plotconfig.displayMFI).prop("checked", false);
+ $(plotconfig.displayvalues).prop("checked", false);
+ $(plotconfig.mrkrSelectj).prop("checked", true);
+ $(plotconfig.mrkrSelectAll).prop("checked",true);
+ }
+ updateCSplots(plotconfig);
+ });
+
+ if (plotconfig.hasOwnProperty("mtable")){
+ $(plotconfig.displayMFI).on("click", function(){
+ updateCSplots(plotconfig);
+ });
+ $(plotconfig.displayvalues).on("click", function(){
+ updateCSplots(plotconfig);
+ });
+ }
+ $(plotconfig.toggledisplayj).on("click",function() {
+ plotconfig.selectedPopulations = [];
+ $(plotconfig.popSelectj).each(function() {
+ if (this.checked) {
+ plotconfig.selectedPopulations.push(parseInt(this.value));
+ }
+ })
+ if (plotconfig.hasOwnProperty("mtable")){
+ plotconfig.selectedMarkers = [];
+ $(plotconfig.mrkrSelectj).each(function() {
+ if (this.checked) {
+ plotconfig.selectedMarkers.push(parseInt(this.value));
+ }
+ });
+ var text = document.getElementById(plotconfig.toggledisplay).firstChild;
+ text.data = text.data == "View per marker" ? "View per population" : "View per marker";
+ plotconfig.view = plotconfig.view == "p" ? "m" : "p";
+ updateBoxplot(plotconfig);
+ } else {
+ var imgSrc = document.getElementById(plotconfig.toggledisplay);
+ imgSrc.src = imgSrc.src.endsWith("stackedsm.png") ? "/static/images/flowtools/barssm.png" : "/static/images/flowtools/stackedsm.png";
+ plotconfig.type = plotconfig.type == "barplot" ? "areaplot" : "barplot";
+ updatePlot(plotconfig);
+ }
+ });
+ displayPlot(plotconfig);
+};
+
+var displayPlot = function(plotconfig) {
+ var h = $(window).height() - 200;
+ $(plotconfig.plotdivj).empty();
+ $(plotconfig.plotdivj).height(h);
+
+ if (plotconfig.hasOwnProperty("mtable")) {
+ var nbPop = Object.keys(plotconfig.csdata.mfi[plotconfig.mrkrNames[0]]).length + 2;
+ // Get Markers too
+ for (var i = 0, nbMarkers = plotconfig.mrkrNames.length; i < nbMarkers; i++) {
+ plotconfig.allMarkers.push(i);
+ plotconfig.selectedMarkers.push(i);
+ }
+ } else {
+ var nbPop = plotconfig.csdata[0].length;
+ }
+
+ for (var i = 2; i < nbPop; i++) {
+ plotconfig.allPopulations.push(i - 1);
+ plotconfig.selectedPopulations.push(i - 1);
+ }
+
+ $(window).on('resize',function() {
+ waitForFinalEvent(function() {
+ if (plotconfig.hasOwnProperty("mtable")){
+ updateBoxplot(plotconfig);
+ } else {
+ updatePlot(plotconfig);
+ }
+ }, 500, "resizePlot");
+ });
+
+ displayPopulationLegend(plotconfig);
+ if (plotconfig.hasOwnProperty("mtable")){
+ displayMarkerTable(plotconfig);
+ updateBoxplot(plotconfig);
+ } else {
+ updatePlot(plotconfig);
+ }
+};
+
+var updatePlot = function(plotconfig) {
+ var h = $(window).height() - 200,
+ traces = [],
+ tmptraces = [],
+ x_values = [],
+ totals = [];
+ layout = {};
+
+ $(plotconfig.plotdivj).empty();
+ $(plotconfig.plotdivj).height(h);
+ for (var i = 1, j = plotconfig.csdata.length; i < j; i++) {
+ x_values.push(newSmpNames[plotconfig.csdata[i][1]]);
+ }
+
+ for (var k = 1, i = plotconfig.csdata.length; k < i; k++){
+ totals[k] = 0;
+ for (var m = 2, o = plotconfig.csdata[0].length; m < o; m++){
+ for (var n = 0, p = plotconfig.selectedPopulations.length; n < p; n++){
+ if (plotconfig.csdata[0][m] === plotconfig.selectedPopulations[n]) {
+ totals[k] += plotconfig.csdata[k][m];
+ }
+ }
+ }
+ }
+
+ for (var i = 0, ii = plotconfig.selectedPopulations.length; i < ii; i++) {
+ pop = plotconfig.selectedPopulations[i];
+ var popName = "Pop " + pop;
+ var y_values = [];
+ var obj;
+
+ for (var j = 1, jj = plotconfig.csdata.length; j < jj; j++) {
+ var newvalue = (plotconfig.csdata[j][pop + 1] / totals[j]) * 100;
+ y_values.push(newvalue);
+ }
+ if (plotconfig.type === "areaplot") {
+ obj = {
+ x: x_values,
+ y: y_values,
+ hoverinfo: "x",
+ name: popName,
+ type: 'area',
+ fill: 'tonexty',
+ marker: {color: color_palette[0][pop][0]}
+ };
+ }
+ if (plotconfig.type === "barplot") {
+ obj = {
+ x: x_values,
+ y: y_values,
+ hoverinfo: "x",
+ name: popName,
+ type: 'bar',
+ marker: {color: color_palette[0][pop][0]}
+ };
+ }
+ tmptraces.push(obj)
+ }
+
+ if (plotconfig.type === "barplot") {
+ layout = {
+ hovermode:'closest',
+ title: '',
+ barmode: 'stack',
+ showlegend: false,
+ yaxis: {
+ mirror: 'all',
+ tickmode: 'array',
+ ticktext: ["","20%", "40%", "60%", "80%", "100%"],
+ tickvals: [0,20,40,60,80,100],
+ title: 'Populations proportions in selected set',
+ titlefont: {
+ size: 16,
+ color: 'grey'
+ }
+ }
+ };
+ traces = tmptraces;
+ }
+ if (plotconfig.type === "areaplot") {
+ function stacked(trcs) {
+ for(var i=1; i
t<"bottom"lp><"clear">',
+ columnDefs: [{
+ targets: propTargets,
+ className: "dt-body-right",
+ render: function(data, type, row){
+ return parseFloat(data).toFixed(2) + '%';
+ }
+ }, {
+ targets: [smpcol - 1, smpcol, smpcol + 1],
+ className: "dt-body-left",
+ }],
+ buttons: [
+ 'copy', 'pdfHtml5','csvHtml5', 'colvis'
+ ],
+ colReorder: {
+ fixedColumnsLeft:1
+ },
+ select: true
+ });
+
+ // Add titles to File ID and Sample Name
+ $('#proptable tr').each(function(i,d){
+ if (i > 0) {
+ $(this).find('td').each(function(j,e){
+ if (j == 1 ) {
+ $(this).prop('title', fileID[i - 1] );
+ }
+ if (j == 2) {
+ $(this).prop('title', sampleNames[i - 1]);
+ }
+ });
+ }
+ });
+
+ // Add a table below to rename pops
+ // Might want to change that some other time?
+ $('#popnamesDiv').html(popHTML);
+ var popEditor = new $.fn.dataTable.Editor({
+ ajax: popHandle,
+ table: '#popnamestable',
+ fields: popEditorData,
+ idSrc: '1'
+ });
+
+ $('#popnamestable').on( 'click', 'tbody td', function (e) {
+ popEditor.bubble(this);
+ });
+ var popTable = $('#popnamestable').DataTable({
+ columns: popTableHeadings,
+ dom: 't',
+ select: true,
+ data: popTableData
+ });
+
+ smpEditor.on( 'preSubmit', function(e, object, action){
+ var data = object.data;
+ var key = Object.keys(data)[0];
+ var count = object.data[key]['Comment'];
+
+ propTableData.forEach(function(d){
+ if (d.SampleName === key) {
+ d.Comment = count;
+ newSmpNames[key] = count;
+ }
+ });
+ pctablecontent = $.extend(true, [], propTableData);
+ });
+ popEditor.on( 'preSubmit', function(e, object, action){
+ var data = object.data;
+ var key = Object.keys(data['1'])[0];
+ var count = object.data['1'][key];
+ popTableData[0][key] = count;
+ newPopNames[key] = count;
+ });
+ });
+};
+
+var displayStackedAreaPlot = function() {
+ $.ajax({
+ url: url,
+ dataType: "text",
+ success: function(text) {
+ configAreaplot = {
+ displaybutton : '#updateDisplayA',
+ popSelectj : '.popSelectA',
+ plotdivj : '#plotDivA',
+ toggledisplayj : '#togglePlot',
+ toggledisplay : 'toggleButtonImg',
+ csdata : preprocess(text),
+ plotdiv : 'plotDivA',
+ type : 'areaplot',
+ table : '#popTableA tbody',
+ popSelect : 'popSelectA',
+ allPopulations : [],
+ selectedPopulations : [],
+ popSelectAll : '#popSelectAllA',
+ popSelectCheck : '.popSelectA:checked'
+ };
+ displayToolbar(configAreaplot);
+ }
+ });
+};
+
+var displayBoxplot = function() {
+ $.ajax({
+ url: boxplotUrl,
+ dataType: "json",
+ success: function(data) {
+ configBoxplot = {
+ displaybutton : '#updateDisplayC',
+ toggledisplayj : '#changeDisplayC',
+ toggledisplay : 'changeDisplayC',
+ popSelectj : '.popSelectC',
+ plotdivj : '#plotDivC',
+ csdata : data,
+ plotdiv : 'plotDivC',
+ type : 'boxplot',
+ table : '#popTableC tbody',
+ popSelect : 'popSelectC',
+ allMarkers : [],
+ selectedMarkers: [],
+ allPopulations : [],
+ selectedPopulations : [],
+ popSelectAll : '#popSelectAllC',
+ popSelectCheck: '.popSelectC:checked',
+ mrkrSelectAll : '#mrkrSelectAllC',
+ mrkrSelectCheck: '.mrkrSelectC:checked',
+ mrkrSelect : 'mrkrSelectC',
+ mtable : '#mrkrTableC tbody',
+ mrkrSelectj: '.mrkrSelectC',
+ displayvalues: '#displayLabelsC',
+ displayMFI: '#displayMFIC',
+ view: 'p',
+ mrkrNames : Object.keys(data.mfi)
+ };
+ displayToolbar(configBoxplot);
+ }
+ });
+};
diff -r 000000000000 -r 8c17aa8032c2 cs_overview/static/flowtools/js/pCoordCSstats.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cs_overview/static/flowtools/js/pCoordCSstats.js Mon Feb 27 12:48:54 2017 -0500
@@ -0,0 +1,418 @@
+// Copyright (c) 2016 Northrop Grumman.
+// All rights reserved.
+
+/*
+ * Initialize variables for parallelCoordinates display
+*/
+var pcApp = pcApp || {};
+
+pcApp.allSamples = [];
+pcApp.selectedSamples = [];
+pcApp.origData;
+pcApp.flowData;
+pcApp.updatedData;
+pcApp.headers = [];
+pcApp.foreground;
+pcApp.background;
+
+var displayAll = function() {
+ displayParallelPlot();
+}
+/*
+ * Display the Population Legend
+*/
+var displaySmpTable = function() {
+ $('#popTablePC tbody').empty();
+ pcApp.origData.map(function(d) {
+ $('#popTablePC tbody').append('| '
+ + ' | ' + newSmpNames[d.SampleName]
+ + ' | |
');
+ });
+
+ $('#popSelectAllPC').click(function() {
+ var checkAll = $("#popSelectAllPC").prop('checked');
+ if (checkAll) {
+ $(".popSelectPC").prop("checked", true);
+ } else {
+ $(".popSelectPC").prop("checked", false);
+ }
+ pcApp.selectedSamples = [];
+ $('.popSelectPC').each(function() {
+ if (this.checked) {
+ pcApp.selectedSamples.push(parseInt(this.value));
+ }
+ })
+ displayTableGrid();
+ if (checkAll) {
+ displayParallelPlot();
+ } else {
+ updateParallelForeground();
+ }
+ });
+
+ $('.popSelectPC').click(function() {
+ if ($('.popSelectPC').length == $(".popSelectPC:checked").length) {
+ $('#popSelectAllPC').prop("checked",true);
+ } else {
+ $('#popSelectAllPC').prop("checked",false);
+ }
+ pcApp.selectedSamples = [];
+ $('.popSelectPC').each(function() {
+ if (this.checked) {
+ pcApp.selectedSamples.push(parseInt(this.value));
+ }
+ })
+ displayTableGrid();
+ updateParallelForeground();
+ });
+ updateSmpTable();
+};
+
+var updateSmpTable = function() {
+ $('.popSelectPC').each(function() {
+ var smp = parseInt(this.value);
+ if ($.inArray(smp,pcApp.selectedSamples) > -1) {
+ this.checked = true;
+ } else {
+ this.checked = false;
+ }
+ })
+}
+
+var displayTableGrid = function() {
+ var colTable = [],
+ colNames = [],
+ pctargets = [],
+ updatedHeaders = [],
+ displayData = [],
+ targetCol = 0,
+ textCol = [],
+ colOrder = [],
+ tableHTML = [];
+
+ $("#tableDivPC").empty();
+ pcApp.updatedData = $.extend(true,[],pctablecontent);
+ pcApp.updatedData.forEach(function(d, idx){
+ d.SampleName = idx + 1;
+ delete(d.FileID);
+ });
+
+ updatedHeaders = Object.keys(pcApp.updatedData[0]);
+ displayData = pcApp.updatedData.filter(function(d,i) {
+ if ($.inArray(i,pcApp.selectedSamples) > -1) {
+ return d;
+ }
+ });
+
+ targetCol = updatedHeaders.length - 2;
+ updatedHeaders.forEach(function(d,i){
+ colTable.push("" + d + " | ");
+ colNames.push({"data":d});
+ if (i < targetCol){
+ pctargets.push(i);
+ }
+ });
+ textCol = [targetCol, targetCol + 1];
+ colOrder = textCol.concat(pctargets);
+ tableHTML = [
+ '',
+ '',
+ '',
+ colTable.join("\n"),
+ '
',
+ '',
+ '
',
+ ];
+
+ $('#tableDivPC').html(tableHTML.join("\n"));
+ var pcTable = $('#pcTable').DataTable({
+ columns: colNames,
+ data: displayData,
+ order: [[ targetCol, "asc" ]],
+ pageLength: 10,
+ //paging: false,
+ scrollY: 250,
+ scrollCollapse: true,
+ scrollX: true,
+ dom: '<"top"B>t<"bottom"lip><"clear">',
+ columnDefs: [{
+ targets: pctargets,
+ className: "dt-body-right",
+ render: function(data,type,row){
+ return parseFloat(data).toFixed(2) + '%';
+ }
+ }, {
+ targets: [targetCol, targetCol+1],
+ className: "dt-body-center"
+ }, {
+ targets:[targetCol],
+ render: function(data, type, row){
+ return 'Sample' + parseInt(data);
+ }
+ }],
+ buttons: [
+ 'copy', 'pdfHtml5','csvHtml5', 'colvis'
+ ],
+ colReorder: {order:colOrder},
+ select: true
+ });
+
+ $('#pcTable').on('mouseover', 'tr', function() {
+ var data = pcTable.row(this).data();
+ if (data != undefined) {
+ var smp = parseInt(data.SampleName) - 1;
+ pcApp.selectedSamples = [smp];
+ updateParallelForeground();
+ }
+ });
+ $('#pcTable').on('mouseleave', 'tr', function() {
+ pcApp.selectedSamples = [];
+ $('.popSelectPC').each(function() {
+ if (this.checked) {
+ pcApp.selectedSamples.push(parseInt(this.value));
+ }
+ updateParallelForeground();
+ })
+ });
+};
+/*
+ * Display The Main Plot
+*/
+var displayParallelPlot = function() {
+ var margin = {top: 30, right: 10, bottom: 10, left: 10},
+ h = 300,
+ w = $("#plotDivPC").width(),
+ width = w - margin.left - margin.right,
+ height = h - margin.top - margin.bottom,
+ y = {},
+ dragging = {},
+ ymax = 0;
+
+ $("#plotDivPC").empty();
+ $("#plotDivPC").height(h);
+ var svg = d3.select("#plotDivPC").append("svg")
+ .attr("width", width + margin.left + margin.right)
+ .attr("height", height + margin.top + margin.bottom)
+ .append("g")
+ .attr("transform", "translate(" + margin.left + "," + margin.top + ")")
+
+ var x = d3.scale.ordinal().rangePoints([0, width], 1);
+ var line = d3.svg.line();
+ var axis = d3.svg.axis()
+ .orient("left")
+ .tickFormat(d3.format("d"))
+ .ticks(5);
+
+ for (var m = 0, n = pcApp.flowData.length; m < n; m++){
+ for (var p in pcApp.flowData[m]){
+ if (+pcApp.flowData[m][p] > ymax){
+ ymax = +pcApp.flowData[m][p];
+ }
+ }
+ }
+
+ // Y axis label
+ svg.append("text")
+ .attr("class", "ylabel")
+ .attr("transform", "rotate(-90)")
+ .attr("y", 0 - margin.left)
+ .attr("x",0 - (height / 2))
+ .attr("dy", "1em")
+ .style("text-anchor", "middle")
+ .text("Fraction of population in sample");
+
+ var dimensions = d3.keys(pcApp.flowData[0]).filter(function(d) {
+ return (y[d] = d3.scale.linear()
+ .domain([0,parseInt(ymax)+1])
+ .range([height, 0]));
+ });
+ x.domain(dimensions);
+
+ function path(d) {
+ return line(dimensions.map(function(p) { return [x(p), y[p](d[p])]; }));
+ }
+
+ function position(d) {
+ var v = dragging[d];
+ return v == null ? x(d) : v;
+ }
+
+ function transition(g) {
+ return g.transition().duration(500);
+ }
+
+ function brush() {
+ var actives = dimensions.filter(function(p) { return !y[p].brush.empty(); });
+ var extents = actives.map(function(p) { return y[p].brush.extent(); });
+ var selectedSamples = pcApp.origData.filter(function(d) {
+ var smp = parseInt(d.SampleNumber);
+ var tf = actives.every(function(p,i) {
+ return extents[i][0] <= pcApp.flowData[smp][p] &&
+ pcApp.flowData[smp][p] <= extents[i][1];
+ });
+ if (tf) {
+ return smp.toString();
+ }
+ });
+ pcApp.selectedSamples = selectedSamples.map(function(d) {
+ return parseInt(d.SampleNumber);
+ });
+
+ updateParallelForeground();
+ updateSmpTable()
+ displayTableGrid();
+ }
+ // Display paths in light gray color, to use as reference
+ pcApp.background = svg.append("g")
+ .attr("class", "background")
+ .selectAll("path")
+ .data(pcApp.flowData)
+ .enter().append("path")
+ .attr("d", path);
+
+ // Add foreground lines for focus, color by population.
+ pcApp.foreground = svg.append("g")
+ .attr("class", "foreground")
+ .selectAll("path")
+ .data(pcApp.origData)
+ .enter().append("path")
+ .attr("d", function(d) {
+ var smp = d.SampleNumber;
+ return path(pcApp.flowData[smp]); })
+ .attr("stroke",function(d){
+ var smp = d.SampleNumber + 1;
+ return color_palette[0][smp][0];})
+ .attr("stroke-width", 1);
+
+ // Add a group element for each dimension.
+ var g = svg.selectAll(".dimension")
+ .data(dimensions)
+ .enter().append("g")
+ .attr("class", "dimension")
+ .attr("transform", function(d) { return "translate(" + x(d) + ")"; })
+ .call(d3.behavior.drag()
+ .origin(function(d) { return {x: x(d)}; })
+ .on("dragstart", function(d) {
+ dragging[d] = x(d);
+ pcApp.background.attr("visibility", "hidden");})
+ .on("drag", function(d) {
+ dragging[d] = Math.min(width, Math.max(0, d3.event.x));
+ pcApp.foreground.attr("d", path);
+ dimensions.sort(function(a, b) { return position(a) - position(b); });
+ x.domain(dimensions);
+ g.attr("transform", function(d) { return "translate(" + position(d) + ")"; }); })
+ .on("dragend", function(d) {
+ delete dragging[d];
+ transition(d3.select(this)).attr("transform", "translate(" + x(d) + ")");
+ transition(pcApp.foreground).attr("d", path);
+ pcApp.background
+ .attr("d", path)
+ .transition()
+ .delay(500)
+ .duration(0)
+ .attr("visibility", null);
+ }));
+
+ // Add an axis and title.
+ g.append("g")
+ .attr("class", "axis")
+ .each(function(d) { d3.select(this).call(axis.scale(y[d])); });
+ g.append("g")
+ .attr("class", "xlabel")
+ .append("text")
+ .style("text-anchor", "middle")
+ .attr("y", -9)
+ .text(function(d) { return d; });
+
+ // Add and store a brush for each axis.
+ g.append("g")
+ .attr("class", "brush")
+ .each(function(d) { d3.select(this).call(y[d].brush = d3.svg.brush().y(y[d]).on("brush", brush)); })
+ .selectAll("rect")
+ .attr("x", -8)
+ .attr("width", 16);
+
+ // Control line opacity.
+ $('#PCline_opacity').on('change', (function() {
+ var val = $(this).val();
+ $('#plotDivPC .foreground path').css('stroke-opacity', val.toString());
+ $('#pc_opacity').html((Math.round(val*10000)/100) + "%");
+ }));
+};
+
+var updateParallelForeground = function() {
+ pcApp.foreground[0].map(function(d) {
+ var smp = parseInt(d['__data__']['SampleNumber'])
+ if ($.inArray(smp,pcApp.selectedSamples) < 0) {
+ d.style.display = "none";
+ } else {
+ d.style.display = null;
+ }
+ });
+};
+/*
+ * Retrieve the data, then call display functions
+*/
+var displayParallelCoordinates = function() {
+/* var inputFile = "./csOverview.tsv";
+ d3.tsv(inputFile, function(error, data) {
+ if (error) {
+ alert("Problem Retrieving Data");
+ return;
+ }
+ */
+ pcApp.origData = $.extend(true,[], pctablecontent);
+ pcApp.headers = Object.keys(pcApp.origData[0]);
+ pcApp.headers.splice(pcApp.headers.indexOf("FileID"), 1);
+ pcApp.origData.forEach(function(d,idx){
+ d.SampleNumber = idx;
+// delete d.FileID;
+ })
+ /*
+ * For the plot use only the proportion of each
+ * population per sample. Store in flowData
+ */
+ pcApp.flowData = $.extend(true,[],pctablecontent);
+ pcApp.flowData.forEach(function(d,idx){
+ delete d.SampleName;
+ delete d.FileID;
+ delete d.Comment;
+ });
+ for (var i = 0, j = pcApp.flowData.length; i < j ; i++) {
+ pcApp.allSamples.push(i);
+ pcApp.selectedSamples.push(i);
+ }
+ displaySmpTable();
+ displayTableGrid();
+ displayParallelPlot();
+
+ $("#resetPCDisplay").on("click",function() {
+ var opcty = ".8";
+ for (var i = 0, j = pcApp.flowData.length; i < j; i++) {
+ pcApp.allSamples.push(i);
+ pcApp.selectedSamples.push(i);
+ }
+ $("#smpSelectAllPC").prop('checked',true);
+ $(".smpSelectPC").prop("checked",true);
+
+ $('#plotDivPC .foreground path').css('stroke-opacity', opcty);
+ $('#pc_opacity').html("80%");
+ $('#PCline_opacity').val(0.8);
+
+ displaySmpTable();
+ displayTableGrid();
+ displayParallelPlot();
+ });
+
+ $(window).on('resize',function() {
+ waitForFinalEvent(function() {
+ displayAll();
+ }, 500, "resizePC");
+ });
+// });
+};
diff -r 000000000000 -r 8c17aa8032c2 cs_overview/static/flowtools/js/pCoordMFIstats.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cs_overview/static/flowtools/js/pCoordMFIstats.js Mon Feb 27 12:48:54 2017 -0500
@@ -0,0 +1,559 @@
+// Copyright (c) 2016 Northrop Grumman.
+// All rights reserved.
+/*
+ * Initialize variables for parallelCoordinates display
+*/
+var pcAppMFI = pcAppMFI || {};
+
+pcAppMFI.origData;
+pcAppMFI.flowData;
+pcAppMFI.background;
+pcAppMFI.foreground;
+pcAppMFI.selectedLines = [];
+pcAppMFI.selectedPopulations = [];
+pcAppMFI.selectedSamples = [];
+pcAppMFI.populations = [];
+pcAppMFI.samples = [];
+pcAppMFI.lines = [];
+pcAppMFI.allLines;
+pcAppMFI.headers = [];
+
+var displayAllm = function() {
+ displayParallelPlotm();
+};
+/*
+ * Display the Population Legend
+*/
+var displayPopTablem = function() {
+ $('#popTablePCm tbody').empty();
+ pcAppMFI.populations.map(function(d, index) {
+ $('#popTablePCm tbody').append('| '
+ + ' | ' + newPopNames[d]
+ + ' | |
');
+ });
+
+ $('#popSelectAllPCm').click(function() {
+ var checkAll = $("#popSelectAllPCm").prop('checked');
+ if (checkAll) {
+ $(".popSelectPCm").prop("checked", true);
+ for (var i = 0; i < pcAppMFI.allLines; i ++) {
+ pcAppMFI.selectedLines.push(i);
+ pcAppMFI.lines.push(i);
+ }
+ } else {
+ $(".popSelectPCm").prop("checked", false);
+ pcAppMFI.selectedLines = [];
+ pcAppMFI.lines = [];
+ }
+
+ pcAppMFI.selectedPopulations = [];
+ $('.popSelectPCm').each(function() {
+ if (this.checked) {
+ pcAppMFI.selectedPopulations.push(parseInt(this.value));
+ }
+ });
+
+ displayTableGridm();
+ if (checkAll) {
+ displayParallelPlotm();
+ } else {
+ updateParallelForegroundidx();
+ }
+ });
+
+ $('.popSelectPCm').click(function() {
+ if ($('.popSelectPCm').length == $(".popSelectPCm:checked").length) {
+ $('#popSelectAllPCm').prop("checked",true);
+ } else {
+ $('#popSelectAllPCm').prop("checked",false);
+ }
+ pcAppMFI.selectedPopulations = [];
+ $('.popSelectPCm').each(function() {
+ if (this.checked) {
+ pcAppMFI.selectedPopulations.push(parseInt(this.value));
+ }
+ });
+ pcAppMFI.selectedLines = [];
+ pcAppMFI.lines = [];
+ pcAppMFI.origData.forEach(function(d,idx){
+ if ($.inArray(pcAppMFI.populations.indexOf(d.Population), pcAppMFI.selectedPopulations) > -1) {
+ if ($.inArray(pcAppMFI.samples.indexOf(d.SmpName), pcAppMFI.selectedSamples) > -1){
+ pcAppMFI.selectedLines.push(idx);
+ pcAppMFI.lines.push(idx);
+ }
+ }
+ });
+ displayTableGridm();
+ updateParallelForegroundidx();
+ });
+ updatePopTableidx();
+ updateSmpTableidx();
+};
+
+var updatePopTableidx = function() {
+ $('.popSelectPCm').each(function() {
+ var pop = parseInt(this.value);
+ var selectedPops = pcAppMFI.origData.map(function(d){
+ if ($.inArray(d.idx, pcAppMFI.selectedLines) > -1){
+ return pcAppMFI.populations.indexOf(d.Population);
+ }
+ });
+ if ($.inArray(pop,selectedPops) > -1) {
+ this.checked = true;
+ } else {
+ this.checked = false;
+ }
+ });
+};
+/*
+* Display Sample Legend
+*/
+var displaySmpTablem = function(){
+ $('#smpTablePCm tbody').empty();
+ pcAppMFI.samples.map(function(d, index) {
+ $('#smpTablePCm tbody').append('| ' + newSmpNames[d]
+ + ' | ' + ' |
');
+ });
+
+ $('#smpSelectAllPCm').click(function() {
+ var checkAll = $("#smpSelectAllPCm").prop('checked');
+ if (checkAll) {
+ $(".smpSelectPCm").prop("checked", true);
+ for (var i = 0; i < pcAppMFI.allLines; i ++) {
+ pcAppMFI.selectedLines.push(i);
+ pcAppMFI.lines.push(i);
+ }
+ } else {
+ $(".smpSelectPCm").prop("checked", false);
+ pcAppMFI.selectedLines = [];
+ pcAppMFI.lines = [];
+ }
+ pcAppMFI.selectedSamples = [];
+ $('.smpSelectPCm').each(function() {
+ if (this.checked) {
+ pcAppMFI.selectedSamples.push(parseInt(this.value));
+ }
+ });
+ displayTableGridm();
+ if (checkAll) {
+ displayParallelPlotm();
+ } else {
+ updateParallelForegroundidx();
+ }
+ });
+
+ $('.smpSelectPCm').click(function() {
+ if ($('.smpSelectPCm').length == $(".smpSelectPCm:checked").length) {
+ $('#smpSelectAllPCm').prop("checked",true);
+ } else {
+ $('#smpSelectAllPCm').prop("checked",false);
+ }
+ pcAppMFI.selectedSamples = [];
+ $('.smpSelectPCm').each(function() {
+ if (this.checked) {
+ pcAppMFI.selectedSamples.push(parseInt(this.value));
+ }
+ });
+ pcAppMFI.selectedLines = [];
+ pcAppMFI.lines = [];
+ pcAppMFI.origData.forEach(function(d,idx) {
+ if ($.inArray(pcAppMFI.populations.indexOf(d.Population), pcAppMFI.selectedPopulations) > -1) {
+ if ($.inArray(pcAppMFI.samples.indexOf(d.SmpName), pcAppMFI.selectedSamples) > -1){
+ pcAppMFI.selectedLines.push(idx);
+ pcAppMFI.lines.push(idx);
+ }
+ }
+ });
+ displayTableGridm();
+ updateParallelForegroundidx();
+ });
+};
+
+var updateSmpTableidx = function() {
+ $('.smpSelectPCm').each(function() {
+ var smp = parseInt(this.value),
+ selectedSamples = pcAppMFI.origData.map(function(d){
+ if ($.inArray(d.idx, pcAppMFI.selectedLines) > -1){
+ return pcAppMFI.samples.indexOf(d.SmpName);
+ }
+ });
+ if ($.inArray(smp,selectedSamples) > -1) {
+ this.checked = true;
+ } else {
+ this.checked = false;
+ }
+ });
+};
+/*
+ * Display Data table
+*/
+var displayTableGridm = function() {
+ var colTablem = [],
+ colNamesm = [],
+ pctargetsm = [],
+ displayDatamfi = [],
+ targetColm = pcAppMFI.headers.length - 3,
+ textColm = [],
+ colOrderm = [],
+ tableHTMLm = [];
+
+ $("#tableDivPCm").empty();
+
+ displayDatamfi = pcAppMFI.origData.filter(function(d,i) {
+ if ($.inArray(i,pcAppMFI.selectedLines) > -1) {
+ return d;
+ }
+ });
+ displayDatamfi.forEach(function(d){
+ d.EditedPopName = newPopNames[d.Population];
+ d.SampleName = newSmpNames[d.SmpName];
+ });
+ pcAppMFI.headers.forEach(function(d,i){
+ colTablem.push("" + d + " | ");
+ colNamesm.push({"data":d});
+ if (i < targetColm - 1){
+ pctargetsm.push(i);
+ }
+ });
+ textColm = [targetColm, targetColm + 1, targetColm + 2];
+ colOrderm = textColm.concat(pctargetsm);
+ colOrderm.push(targetColm - 1);
+ tableHTMLm = [
+ '',
+ '',
+ '',
+ colTablem.join("\n"),
+ '
',
+ '',
+ '
',
+ ];
+ $('#tableDivPCm').html(tableHTMLm.join("\n"));
+ var pcTablem = $('#pcTableMFI').DataTable({
+ columns: colNamesm,
+ data: displayDatamfi,
+ order: [[ targetColm, "asc" ]],
+ pageLength: 10,
+ //paging: false,
+ scrollY: 250,
+ scrollCollapse: true,
+ scrollX: true,
+ dom: '<"top"B>t<"bottom"lip><"clear">',
+ columnDefs: [{
+ targets: pctargetsm,
+ className: "dt-body-right",
+ render: function(data,type,row){
+ return parseFloat(data).toFixed(2);
+ }
+ }, {
+ targets: [targetColm - 1],
+ className: "dt-body-right",
+ render: function(data,type,row){
+ return parseFloat(data).toFixed(2) + '%';
+ }
+ }, {
+ targets: [targetColm, targetColm+1, targetColm+2],
+ className: "dt-body-center"
+ }],
+ buttons: [
+ 'copy', 'pdfHtml5','csvHtml5', 'colvis'
+ ],
+ colReorder: {order:colOrderm},
+ select: true
+ });
+
+ $('#pcTableMFI').on('mouseover', 'tr', function() {
+ var data = pcTablem.row(this).data();
+ if (data != undefined) {
+ var line = parseInt(data.idx);
+ pcAppMFI.selectedLines = [line];
+ updateParallelForegroundidx();
+ }
+ });
+ $('#pcTableMFI').on('mouseleave', 'tr', function() {
+ pcAppMFI.selectedLines = [];
+ for (var i = 0, j = pcAppMFI.lines.length; i < j; i++){
+ pcAppMFI.selectedLines.push(pcAppMFI.lines[i]);
+ }
+ updateParallelForegroundidx();
+ });
+};
+/*
+* Update Parallel Foreground
+*/
+var updateParallelForegroundidx = function() {
+ pcAppMFI.foreground[0].map(function(d) {
+ var ln = parseInt(d['__data__']['idx']);
+
+ if ($.inArray(ln,pcAppMFI.selectedLines) < 0){
+ d.style.display = "none";
+ } else {
+ d.style.display = null;
+ }
+ });
+};
+/*
+ * Display The Main Plot
+*/
+var displayParallelPlotm = function() {
+ var margin = {top: 30, right: 10, bottom: 10, left: 10},
+ h = $("#chartDivPCm").height() * 0.6,
+ w = $("#plotDivPCm").width(),
+ y = {},
+ dragging = {},
+ width = w - margin.left - margin.right,
+ height = h - margin.top - margin.bottom;
+
+ $("#plotDivPCm").empty();
+ $("#plotDivPCm").height(h);
+
+ var svg = d3.select("#plotDivPCm").append("svg")
+ .attr("width", w)
+ .attr("height", h)
+ .append("g")
+ .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+ // Y axis label
+ svg.append("text")
+ .attr("class", "ylabel")
+ .attr("transform", "rotate(-90)")
+ .attr("y", 0 - margin.left)
+ .attr("x", 0 - (height / 2))
+ .attr("dy", "1em")
+ .style("text-anchor", "middle")
+ .text("MFI");
+
+ var x = d3.scale.ordinal().rangePoints([0, width], 1);
+ var line = d3.svg.line();
+ var axis = d3.svg.axis().orient("left").ticks(8);
+
+ // Use this to scale line width to percentage population
+ var pd = d3.extent(pcAppMFI.origData, function(p) { return +p['Percentage']; });
+ var popScale = d3.scale.linear().range([1,5]).domain(pd);
+
+ var dimensions = d3.keys(pcAppMFI.flowData[0]).filter(function(d) {
+ return (y[d] = d3.scale.linear()
+ .domain(d3.extent(pcAppMFI.flowData,function(p) { return +p[d]; }))
+ .range([height, 0]));
+ });
+ x.domain(dimensions);
+
+ function path(d) {
+ return line(dimensions.map(function(p) { return [x(p), y[p](d[p])]; }));
+ }
+ function position(d) {
+ var v = dragging[d];
+ return v == null ? x(d) : v;
+ }
+ function transition(g) {
+ return g.transition().duration(500);
+ }
+
+ function brush() {
+ var actives = dimensions.filter(function(p) { return !y[p].brush.empty(); });
+ var extents = actives.map(function(p) { return y[p].brush.extent(); });
+ var indices = pcAppMFI.origData.filter(function(d) {
+ var line = parseInt(d.idx)
+ var tf = actives.every(function(p,i) {
+ return extents[i][0] <= pcAppMFI.flowData[line][p] &&
+ pcAppMFI.flowData[line][p] <= extents[i][1];
+ });
+ if (tf) {
+ return line.toString();
+ }
+ });
+
+ pcAppMFI.selectedLines = indices.map(function(d) {
+ return parseInt(d.idx);
+ });
+ pcAppMFI.lines = indices.map(function(d) {
+ return parseInt(d.idx);
+ });
+ updateParallelForegroundidx();
+ updatePopTableidx();
+ updateSmpTableidx();
+ displayTableGridm();
+ }
+
+ // Display paths in light gray color, to use as reference
+ pcAppMFI.background = svg.append("g")
+ .attr("class", "background")
+ .selectAll("path")
+ .data(pcAppMFI.flowData)
+ .enter().append("path")
+ .attr("d", path);
+
+ // Add foreground lines for focus, color by population.
+ pcAppMFI.foreground = svg.append("g")
+ .attr("class", "foreground")
+ .selectAll("path")
+ .data(pcAppMFI.origData)
+ .enter().append("path")
+ .attr("d", path)
+ .attr("stroke",function(d){
+ var pop = pcAppMFI.populations.indexOf(d.Population) + 1;
+ return color_palette[0][pop][0]; })
+ //.attr("stroke-width", 1);
+ // Use this if you want to scale the lines based on
+ // population percentage
+ .attr("stroke-width", function(d) {
+ var pop = pcAppMFI.populations.indexOf(d.Population);
+ var w = popScale(pcAppMFI.origData[pop]['Percentage']);
+ w = parseInt(w);
+ return w;
+ });
+
+ // Add a group element for each dimension.
+ var g = svg.selectAll(".dimension")
+ .data(dimensions)
+ .enter().append("g")
+ .attr("class", "dimension")
+ .attr("transform", function(d) { return "translate(" + x(d) + ")"; })
+ .call(d3.behavior.drag()
+ .origin(function(d) { return {x: x(d)}; })
+ .on("dragstart", function(d) {
+ dragging[d] = x(d);
+ pcAppMFI.background.attr("visibility", "hidden"); })
+ .on("drag", function(d) {
+ dragging[d] = Math.min(width, Math.max(0, d3.event.x));
+ pcAppMFI.foreground.attr("d", path);
+ dimensions.sort(function(a, b) { return position(a) - position(b); });
+ x.domain(dimensions);
+ g.attr("transform", function(d) { return "translate(" + position(d) + ")"; }); })
+ .on("dragend", function(d) {
+ delete dragging[d];
+ transition(d3.select(this)).attr("transform", "translate(" + x(d) + ")");
+ transition(pcAppMFI.foreground).attr("d", path);
+ pcAppMFI.background
+ .attr("d", path)
+ .transition()
+ .delay(500)
+ .duration(0)
+ .attr("visibility", null);
+ }));
+
+ // Add an axis and title.
+ g.append("g")
+ .attr("class", "axis")
+ .each(function(d) { d3.select(this).call(axis.scale(y[d])); });
+ g.append("g")
+ .attr("class", "xlabel")
+ .append("text")
+ .style("text-anchor", "middle")
+ .attr("y", -9)
+ .text(function(d) { return d; });
+
+ // Add and store a brush for each axis.
+ g.append("g")
+ .attr("class", "brush")
+ .each(function(d) { d3.select(this).call(y[d].brush = d3.svg.brush().y(y[d]).on("brush", brush)); })
+ .selectAll("rect")
+ .attr("x", -8)
+ .attr("width", 16);
+
+ // Control line opacity.
+ $('#PCmline_opacity').on('change', (function() {
+ var val = $(this).val();
+ $('#plotDivPCm .foreground path').css('stroke-opacity', val.toString());
+ $('#pcm_opacity').html((Math.round(val*10000)/100) + "%");
+ }));
+};
+
+/*
+ * Retrieve the data, then call display functions
+*/
+var displayParallelCoordinatesMFI = function() {
+ var inputFile = "./csAllMFIs.tsv";
+ d3.tsv(inputFile, function(error, data) {
+ var allPops = 0,
+ allSamples = 0;
+ if (error) {
+ alert("Problem Retrieving Data");
+ return;
+ }
+ pcAppMFI.origData = $.extend(true,[],data);
+ pcAppMFI.headers = Object.keys(pcAppMFI.origData[0]);
+ pcAppMFI.headers.push("EditedPopName");
+ pcAppMFI.origData.forEach(function(d,idx) {
+ d.idx = idx;
+ d.EditedPopName = d.Population;
+ d.SmpName = d.SampleName;
+ pcAppMFI.selectedLines.push(idx);
+ pcAppMFI.lines.push(idx);
+ if (!pcAppMFI.populations.includes(d.Population)){
+ pcAppMFI.populations.push(d.Population);
+ }
+ if (!pcAppMFI.samples.includes(d.SmpName)){
+ pcAppMFI.samples.push(d.SmpName);
+ }
+ });
+ pcAppMFI.populations = pcAppMFI.populations.sort(function(a, b){return a-b});
+ pcAppMFI.allLines = pcAppMFI.origData.length;
+
+ allPops = pcAppMFI.populations.length;
+ allSamples = pcAppMFI.samples.length;
+ for (var i = 0; i < allPops; i++) {
+ pcAppMFI.selectedPopulations.push(i);
+ }
+ for (var i = 0; i < allSamples; i++) {
+ pcAppMFI.selectedSamples.push(i);
+ }
+ /*
+ * For the plot use only the MFI information
+ * for each populations. Store in flowData
+ */
+ pcAppMFI.flowData = $.extend(true,[],data);
+ pcAppMFI.flowData.forEach(function(d) {
+ delete d['Population'];
+ delete d['SampleName'];
+ delete d['Percentage'];
+ });
+
+ displayPopTablem();
+ displaySmpTablem();
+ displayTableGridm();
+ displayParallelPlotm();
+
+ $("#resetDisplayMFIpop").on("click",function() {
+ var opcty = ".8";
+ for (var i = 0; i < allPops; i++) {
+ pcAppMFI.selectedPopulations.push(i);
+ }
+ for (var i = 0; i < allSamples; i++) {
+ pcAppMFI.selectedSamples.push(i);
+ }
+ for (var i = 0; i < pcAppMFI.allLines; i++) {
+ pcAppMFI.selectedLines.push(i);
+ pcAppMFI.lines.push(i);
+ }
+
+ $("#popSelectAllPCm").prop('checked',true);
+ $(".popSelectPCm").prop("checked",true);
+ $("#smpSelectAllPCm").prop('checked',true);
+ $(".smpSelectPCm").prop("checked",true);
+
+ $('#plotDivPCm .foreground path').css('stroke-opacity', opcty);
+ $('#pcm_opacity').html("80%");
+ $('#PCmline_opacity').val(0.8);
+
+ displayPopTablem();
+ displaySmpTablem();
+ displayTableGridm();
+ displayParallelPlotm();
+ });
+
+ $(window).on('resize',function() {
+ waitForFinalEvent(function() {
+ displayAllm();
+ }, 500, "resizePCm");
+ });
+ });
+};
diff -r 000000000000 -r 8c17aa8032c2 cs_overview/static/images/flowtools/barssm.png
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diff -r 000000000000 -r 8c17aa8032c2 cs_overview/static/images/flowtools/pcpop.png
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diff -r 000000000000 -r 8c17aa8032c2 cs_overview/templates/csOverview.template
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cs_overview/templates/csOverview.template Mon Feb 27 12:48:54 2017 -0500
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+CrossSample Overview
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Population Distribution
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+ Edit population names below:
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+ Opacity: 80%
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+ Opacity: 80%
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Display values
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Display MFI
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+ Only 5 markers can be displayed at most.
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+ The number of outliers is too large to display. Representation shows randomly downsampled outliers.
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