annotate js/pCoordCSstats.js @ 2:a64ece32a01a draft default tip

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

// 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('<tr><td align="center">'
        + '<input type="checkbox" id="' + d.SampleName + '" '
        + 'checked class="popSelectPC" value='
        + d.SampleNumber + '/></td><td title="' + newSmpNames[d.SampleName]
        + '">' + newSmpNames[d.SampleName]
        + '</td><td><span style="background-color:'
        + color_palette[0][d.SampleNumber + 1][0]
        + '">&nbsp;&nbsp;&nbsp;</span></td></tr>');
  });

  $('#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("<th>" + d + "</th>");
    colNames.push({"data":d});
    if (i < targetCol){
      pctargets.push(i);
    }
  });
  textCol = [targetCol, targetCol + 1];
  colOrder = textCol.concat(pctargets);
  tableHTML = [
      '<table id="pcTable" class="pctable display compact nowrap" cellspacing="0" width="100%">',
      '<thead>',
      '<tr>',
      colTable.join("\n"),
      '</tr>',
      '</thead>',
      '</table>',
  ];

  $('#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");
  });
//    });
};