diff js/overview.js @ 1:b5453d07f740 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/js/overview.js	Wed Jul 29 17:03:53 2020 -0400
@@ -0,0 +1,325 @@
+// Copyright (c) 2016 Northrop Grumman.
+// All rights reserved.
+
+var scatterData2D = {};
+var scatterData3D = {};
+var scatterData3DMFI = {};
+var scatterDataMFI = {};
+var tableContent;
+var newNames ={};
+var configbp = {};
+var bpurl = "./boxplotData.json";
+
+var waitForFinalEvent = (function () {
+  var timers = {};
+  return function (callback, ms, uniqueId) {
+    if (!uniqueId) {
+      uniqueId = "Don't call this twice without a uniqueId";
+    }
+    if (timers[uniqueId]) {
+      clearTimeout (timers[uniqueId]);
+    }
+    timers[uniqueId] = setTimeout(callback, ms);
+  };
+})();
+
+var updateOverviewPlotDisplay = function(data) {
+  $('#overviewPlotDiv').empty();
+  $('#overviewPlotDiv').html(data);
+};
+
+var displayMFI = function() {
+  var url = "flow.mfi_pop";
+  d3.text(url, function(error, data){
+    var mfiHdgs = [],
+        pp = [],
+        mfiTableData = [],
+        mfiTableHeadings = [],
+        mfiTargets = [],
+        mfiTableHTML = '<table id="mfitable" class="dtable display compact" cellspacing="0" width="100%"/>',
+        popcol = 1,
+        mfiEditorData =[];
+
+    if (error){
+      alert("Problem retrieving data");
+      return;
+    }
+    mfiHdgs = data.split("\n")[0].split("\t");
+    pp = mfiHdgs.pop();
+    mfiHdgs.unshift(pp);
+    mfiHdgs.unshift("Comment");
+    data = d3.tsv.parse(data);
+    function handleSubmit(method, url, d, successCallBack, errorCallBack) {
+      var output = {data : mfiTableData};
+      successCallBack(output);
+    }
+
+    $('#mfiDiv').empty();
+    mfiTableData = $.extend(true,[],data);
+    mfiTableData.forEach(function(d){
+      d.Comment = d.Population;
+      newNames[parseInt(d.Population)] = d.Comment;
+    });
+    //var mfiData = mfiTableData.filter(function(d){return d});
+    tableContent = $.extend(true, [], mfiTableData);
+    mfiHdgs.forEach(function(d,i) {
+      mfiTableHeadings.push({"data": d, "title": d});
+      mfiEditorData.push({"label" : d, "name" : d});
+    });
+
+    for (var i = 2, j = mfiHdgs.length - 2; i<j; i++){
+      mfiTargets.push(i);
+    }
+
+    $('#mfiDiv').html(mfiTableHTML);
+    var editor = new $.fn.dataTable.Editor({
+        ajax: handleSubmit,
+        table: '#mfitable',
+        fields: mfiEditorData,
+        idSrc: 'Population'
+    });
+    $('#mfitable').on('click', 'tbody td:first-child', function (e) {
+      editor.bubble(this);
+    });
+    var mfiTable = $('#mfitable').DataTable({
+        columns: mfiTableHeadings,
+        data: mfiTableData,
+        order: [[ popcol, "asc" ]],
+        pageLength: 25,
+        dom: '<"top"Bi>t<"bottom"lp><"clear">',
+        columnDefs: [{
+            targets: mfiTargets,
+            className: "dt-body-right",
+            render: function(data, type, row){
+              return parseFloat(data).toFixed(2);
+            }
+          }, {
+            targets: [mfiHdgs.length - 2],
+            className: "dt-body-right"
+          }, {
+            targets: [mfiHdgs.length-1],
+            className: "dt-body-right",
+            render: function(data, type, row){
+                    return parseFloat(data).toFixed(2) + '%';
+            }
+          }
+        ],
+        buttons: [
+            'copy', 'pdfHtml5','csvHtml5', 'colvis'
+        ],
+        colReorder: {fixedColumnsLeft:1},
+        select: true
+    });
+    editor.on('preSubmit', function(e, object, action){
+      var data = object.data;
+      var key = Object.keys(data)[0];
+      var count = object.data[key]['Comment'];
+      mfiTableData.forEach(function(d) {
+        if (d.Population === key) {
+          d.Comment = count;
+          newNames[parseInt(d.Population)] = count;
+        }
+      });
+      tableContent = $.extend(true, [], mfiTableData);
+    });
+  });
+};
+
+var displayOverviewPlot = function() {
+  var url = "flow.overview";
+  $.ajax({
+    url: url,
+    dataType: "text",
+    success: function(data) {
+      updateOverviewPlotDisplay(data);
+    }
+  });
+};
+
+var displayScatter2D = function() {
+  var url = "flow.sample";
+  $.ajax({
+    url: url,
+    dataType: "text",
+    success: function(text) {
+      var mfi_url = "flow.mfi_pop";
+      $.ajax({
+        url: mfi_url,
+        dataType: "text",
+        success: function(mfi_text) {
+          scatterDataMFI = new processMFI(mfi_text);
+          scatterData2D = new processData(text);
+          displayScatterToolbar2D();
+          displayScatterPopulation2D();
+          processScatterData2D();
+          processScatterDataMFI2D();
+          displayScatterPlot2D();
+          $(window).on('resize',function() {
+            waitForFinalEvent(function() {
+              processScatterData2D();
+              displayScatterPlot2D();
+            }, 500, "resize2D");
+          });
+        }
+      });
+    }
+  });
+};
+
+var displayScatter3D = function() {
+  var url = "flow.sample";
+  $.ajax({
+    url: url,
+    dataType: "text",
+    success: function(text) {
+      var mfi_url = "flow.mfi_pop";
+      $.ajax({
+        url: mfi_url,
+        dataType: "text",
+        success: function(mfi_text) {
+          scatterData3DMFI = new processMFI(mfi_text);
+          scatterData3D = new processData(text);
+          displayScatterToolbar3D();
+          displayScatterPopulation3D();
+          processScatterData3D();
+          processScatterData3DMFI();
+          displayScatterPlot3D();
+          $(window).on('resize',function() {
+            waitForFinalEvent(function() {
+              processScatterData3D();
+              displayScatterPlot3D();
+            }, 500, "resize3D");
+          });
+        }
+      });
+    }
+  });
+};
+
+var displayMFIBoxplot = function() {
+  $.ajax({
+    url: bpurl,
+    dataType: "json",
+    success: function(data) {
+      configbp = {
+        displaybutton : '#updateDisplaybp',
+        toggledisplayj : '#changeDisplay',
+        toggledisplay : 'changeDisplay',
+        popSelectj : '.popSelectbp',
+        plotdivj : '#plotDivbp',
+        csdata : data,
+        plotdiv : 'plotDivbp',
+        type : 'boxplot',
+        table : '#popTablebp tbody',
+        popSelect : 'popSelectbp',
+        allMarkers : [],
+        selectedMarkers: [],
+        allPopulations : [],
+        selectedPopulations : [],
+        popSelectAll : '#popSelectAllbp',
+        popSelectCheck: '.popSelectbp:checked',
+        mrkrSelectAll : '#mrkrSelectAll',
+        mrkrSelectCheck: '.mrkrSelect:checked',
+        mrkrSelect : 'mrkrSelect',
+        mtable : '#mrkrTable tbody',
+        mrkrSelectj: '.mrkrSelect',
+        displayvalues: '#displayLabels',
+        displayMFI: '#displayMFI',
+        view: 'p',
+        mrkrNames :  Object.keys(data.mfi)
+      };
+      displayToolbar(configbp);
+    }
+  });
+};
+
+function processData(text) {
+  var data = d3.tsv.parseRows(text).map(function(row) {
+    return row.map(function(value) {
+      if (isNaN(value)) {
+        return value;
+      }
+      return +value;
+    });
+  });
+
+  this.columnHeadings = data.shift();
+  this.columnHeadings.pop();
+  var popCol = data[0].length - 1;
+  var p = data.map(function(value,index) {
+    return parseInt(value[popCol]);
+  });
+
+  var populations = {};
+  for (var i = 0; i < p.length; i++) {
+    if (populations[p[i]] === undefined) {
+      populations[p[i]] = 1;
+    } else {
+      populations[p[i]] = populations[p[i]] + 1;
+    }
+  }
+
+  this.popCol = popCol;
+  this.populations = d3.set(p).values();
+  this.populations = this.populations.map(function(value,index) {
+    return parseInt(value);
+  });
+  this.selectedPopulations = this.populations;
+  this.percent = this.populations.map(function(value,index) {
+    return Math.floor(populations[value] * 10000.0 / data.length) / 100.0;
+  });
+
+  this.data = data;
+  this.m1 = 0;
+  this.m2 = 1;
+  this.m3 = 2;
+  this.view = 1;
+};
+
+function processMFI(text) {
+  data = d3.tsv.parseRows(text).map(function(row) {
+    return row.map(function(value) {
+      if (isNaN(value)) {
+        return value;
+      }
+      return +value;
+    });
+  });
+
+  // Get the Headings Row, then remove the Count, Percentage and
+  // Population headings
+  this.columnHeadings = data.shift();
+  this.columnHeadings.pop();
+  this.columnHeadings.pop();
+  this.columnHeadings.pop();
+
+  var popCol = data[0].length -1;
+  var pop = data.map(function(value,index) {
+    return parseInt(value[popCol]);
+  });
+
+  var perCol = data[0].length -2;
+  var per = data.map(function(value,index) {
+    return parseFloat(value[perCol]);
+  });
+
+  var countCol = data[0].length -3;
+  var count = data.map(function(value,index) {
+    return parseInt(value[countCol]);
+  });
+
+  this.popCol = popCol;
+  this.populations = pop;
+  this.selectedPopulations = pop;
+  this.percent = per;
+  this.counts = count;
+
+  var l = data[0].length;
+  this.data = data.map(function(row) {
+    return row.splice(0,countCol);
+  });
+  this.poplist = pop;
+  this.m1 = 0;
+  this.m2 = 1;
+  this.m3 = 2;
+};