diff js/boxplots.js @ 2:a64ece32a01a draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/js/boxplots.js	Tue Jul 28 08:32:36 2020 -0400
@@ -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('<tr>'
+        + '<td><span style="background-color:rgba(0,0,0,' + (v + 1 )/ nbm + ')'
+        + '">&nbsp;&nbsp;&nbsp;</span></td>'
+        + '<td title="' + plotconfig.mrkrNames[v] + '">'
+        + plotconfig.mrkrNames[v] + '</td>'
+        + '<td align="center"><input type="checkbox" checked class='
+        + plotconfig.mrkrSelect + ' value=' + v + '/></td></tr>');
+  });
+  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;
+  };
+})();