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

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

1 // Copyright (c) 2016 Northrop Grumman.
2 // All rights reserved.
3 
4 var url = "./csOverview.tsv",
5     boxplotUrl = "./csBoxplotData.json",
6     pctablecontent,
7     newSmpNames= {},
8     newPopNames = {},
9     configBoxplot = {},
10     configAreaplot = {};
11 
12 var waitForFinalEvent = (function () {
13   var timers = {};
14   return function (callback, ms, uniqueId) {
15     if (!uniqueId) {
16       uniqueId = "Don't call this twice without a uniqueId";
17     }
18     if (timers[uniqueId]) {
19       clearTimeout (timers[uniqueId]);
20     }
21     timers[uniqueId] = setTimeout(callback, ms);
22   };
23 })();
24 
25 var preprocess = function(text){
26   var crossSampleData = d3.tsv.parseRows(text).map(function(row) {
27     return row.map(function(value) {
28       if (isNaN(value)) {
29         return value;
30       }
31       return +value;
32     })
33   })
34   return crossSampleData;
35 };
36 
37 var displayProp = function() {
38   d3.text(url, function(error, data) {
39     var fileID = [],
40         sampleNames = [],
41         popTableData = [],
42         propHeadings = [],
43         propTableData = [],
44         propTableHeadings = [],
45         propTargets = [],
46         popTableHeadings = [],
47         propEditorData = [],
48         popEditorData = [],
49         smpcol = 2,
50         propHTML = '<table id="proptable" class="dtable display compact nowrap" cellspacing="0" width="100%"/>',
51         popHTML = '<table id="popnamestable" class="popt dtable display nowrap compact" cellspacing="0" width="100%"/>';
52 
53     if (error) {
54       alert("Problem retrieving data");
55       return;
56     }
57     propHeadings = data.split("\n")[0].split("\t");
58     propHeadings.unshift("Comment");
59     data = d3.tsv.parse(data);
60     function propHandle(method, url, d, successCallBack, errorCallBack) {
61       var output = {data : propTableData};
62       successCallBack(output);
63     }
64 
65     function popHandle(method, url, d, successCallBack, errorCallBack) {
66       var output = {data : popTableData};
67       successCallBack(output);
68     }
69 
70     propTableData = $.extend(true,[],data);
71     propTableData.forEach(function(d) {
72       d.Comment = d.SampleName;
73       newSmpNames[d.SampleName] = d.Comment;
74       fileID.push(d.FileID);
75       sampleNames.push(d.SampleName);
76     });
77 
78     for (var i = 3, j = propHeadings.length; i < j; i++){
79       propTargets.push(i);
80     }
81     propHeadings.forEach(function(d) {
82       propTableHeadings.push({"data":d, "title":d});
83       propEditorData.push({"label":d,"name":d});
84       if (d != 'Comment' && d != 'SampleName' && d != "FileID") {
85         newPopNames[d] = d.toString();
86         popTableHeadings.push({"data":d, "title":d});
87         popEditorData.push({"label":d,"name":d});
88       }
89     });
90     popTableData.push(newPopNames);
91     pctablecontent = $.extend(true,[],propTableData);
92 
93     $('#propDiv').empty();
94     $('#propDiv').html(propHTML);
95     var smpEditor = new $.fn.dataTable.Editor({
96         ajax: propHandle,
97         table: '#proptable',
98         fields: propEditorData,
99         idSrc: 'SampleName'
00     });
01 
02     $('#proptable').on( 'click', 'tbody td:first-child', function (e) {
03       smpEditor.bubble( this );
04     });
05     var propTable = $('#proptable').DataTable({
06         columns: propTableHeadings,
07         data: propTableData,
08         order: [[ smpcol, "asc" ]],
09         pageLength: 10,
10         scrollX: true,
11         scrollCollapse: true,
12         dom: '<"top"Bi>t<"bottom"lp><"clear">',
13         columnDefs: [{
14             targets: propTargets,
15             className: "dt-body-right",
16             render: function(data, type, row){
17                     return parseFloat(data).toFixed(2) + '%';
18             }
19           }, {
20             targets: [smpcol - 1, smpcol, smpcol + 1],
21             className: "dt-body-left",
22         }],
23         buttons: [
24             'copy', 'pdfHtml5','csvHtml5', 'colvis'
25         ],
26         colReorder: {
27             fixedColumnsLeft:1
28         },
29         select: true
30     });
31 
32     // Add titles to File ID and Sample Name
33     $('#proptable tr').each(function(i,d){
34       if (i > 0) {
35         $(this).find('td').each(function(j,e){
36           if (j == 1 ) {
37             $(this).prop('title', fileID[i - 1] );
38           }
39           if (j == 2) {
40             $(this).prop('title', sampleNames[i - 1]);
41           }
42         });
43       }
44     });
45 
46     // Add a table below to rename pops
47     // Might want to change that some other time?
48     $('#popnamesDiv').html(popHTML);
49     var popEditor = new $.fn.dataTable.Editor({
50         ajax: popHandle,
51         table: '#popnamestable',
52         fields: popEditorData,
53         idSrc: '1'
54     });
55 
56     $('#popnamestable').on( 'click', 'tbody td', function (e) {
57       popEditor.bubble(this);
58     });
59     var popTable = $('#popnamestable').DataTable({
60         columns: popTableHeadings,
61         dom: 't',
62         select: true,
63         data: popTableData
64     });
65 
66     smpEditor.on( 'preSubmit', function(e, object, action){
67       var data = object.data;
68       var key = Object.keys(data)[0];
69       var count = object.data[key]['Comment'];
70 
71       propTableData.forEach(function(d){
72         if (d.SampleName === key) {
73           d.Comment = count;
74           newSmpNames[key] = count;
75         }
76       });
77       pctablecontent = $.extend(true, [], propTableData);
78     });
79     popEditor.on( 'preSubmit', function(e, object, action){
80       var data = object.data;
81       var key = Object.keys(data['1'])[0];
82       var count = object.data['1'][key];
83       popTableData[0][key] = count;
84       newPopNames[key] = count;
85     });
86   });
87 };
88 
89 var displayStackedAreaPlot = function() {
90   $.ajax({
91     url: url,
92     dataType: "text",
93     success: function(text) {
94       configAreaplot = {
95         displaybutton : '#updateDisplayA',
96         popSelectj : '.popSelectA',
97         plotdivj : '#plotDivA',
98         toggledisplayj : '#togglePlot',
99         toggledisplay : 'toggleButtonImg',
00         csdata : preprocess(text),
01         plotdiv : 'plotDivA',
02         type : 'areaplot',
03         table : '#popTableA tbody',
04         popSelect : 'popSelectA',
05         allPopulations : [],
06         selectedPopulations : [],
07         popSelectAll : '#popSelectAllA',
08         popSelectCheck : '.popSelectA:checked'
09       };
10       displayToolbar(configAreaplot);
11     }
12   });
13 };
14 
15 var displayBoxplot = function() {
16   $.ajax({
17     url: boxplotUrl,
18     dataType: "json",
19     success: function(data) {
20       configBoxplot = {
21         displaybutton : '#updateDisplayC',
22         toggledisplayj : '#changeDisplayC',
23         toggledisplay : 'changeDisplayC',
24         popSelectj : '.popSelectC',
25         plotdivj : '#plotDivC',
26         csdata : data,
27         plotdiv : 'plotDivC',
28         type : 'boxplot',
29         table : '#popTableC tbody',
30         popSelect : 'popSelectC',
31         allMarkers : [],
32         selectedMarkers: [],
33         allPopulations : [],
34         selectedPopulations : [],
35         popSelectAll : '#popSelectAllC',
36         popSelectCheck: '.popSelectC:checked',
37         mrkrSelectAll : '#mrkrSelectAllC',
38         mrkrSelectCheck: '.mrkrSelectC:checked',
39         mrkrSelect : 'mrkrSelectC',
40         mtable : '#mrkrTableC tbody',
41         mrkrSelectj: '.mrkrSelectC',
42         displayvalues: '#displayLabelsC',
43         displayMFI: '#displayMFIC',
44         view: 'p',
45         mrkrNames :  Object.keys(data.mfi)
46       };
47       displayToolbar(configBoxplot);
48     }
49   });
50 };