├── .gitignore
├── LICENSE
├── Makefile
├── README.md
├── bower.json
├── demo
    ├── test-all.html
    ├── test-cna.html
    ├── test-color.html
    ├── test-dendrogram.html
    ├── test-dispatch.html
    ├── test-graph.html
    ├── test-heatmap.html
    ├── test-mutmtx.html
    ├── test-scatterplot.html
    ├── test-tooltip.html
    ├── test-transcript.html
    └── testData
    │   ├── entireJson.json
    │   ├── example-annotation.json
    │   ├── example-cna-browser.json
    │   ├── example-cna.json
    │   ├── example-dendrogram-N30.json
    │   ├── example-graph.json
    │   ├── example-heatmap.json
    │   ├── example-mutation-matrix.json
    │   ├── example-scatterplot.json
    │   ├── example-transcript.json
    │   ├── example2-mutation-matrix.json
    │   ├── example2-transcript.json
    │   ├── example3-transcript.json
    │   ├── exampleAnnotations.json
    │   ├── extractAnnotationfromwhole.py
    │   ├── extractCNAfromwhole.py
    │   ├── extractMutMtxfromwhole.py
    │   └── extractTranscriptfromwhole.py
├── gd3.js
├── package.json
├── src
    ├── cna
    │   ├── cna.js
    │   ├── cnaChart.js
    │   ├── cnaData.js
    │   ├── cnaStyle.js
    │   └── index.js
    ├── core
    │   ├── class.js
    │   ├── color.js
    │   ├── dataStructures.js
    │   ├── index.js
    │   └── util.js
    ├── dendrogram
    │   ├── dendrogram.js
    │   ├── dendrogramChart.js
    │   ├── dendrogramData.js
    │   ├── dendrogramStyle.js
    │   └── index.js
    ├── dispatch
    │   ├── dispatch.js
    │   └── index.js
    ├── end.js
    ├── gd3.js
    ├── graph
    │   ├── graph.js
    │   ├── graphChart.js
    │   ├── graphData.js
    │   ├── graphStyle.js
    │   └── index.js
    ├── heatmap
    │   ├── heatmap.js
    │   ├── heatmapChart.js
    │   ├── heatmapData.js
    │   ├── heatmapStyle.js
    │   └── index.js
    ├── mutmtx
    │   ├── index.js
    │   ├── mutmtx.js
    │   ├── mutmtxChart.js
    │   ├── mutmtxData.js
    │   └── mutmtxStyle.js
    ├── scatterplot
    │   ├── index.js
    │   ├── scatterplot.js
    │   ├── scatterplotChart.js
    │   ├── scatterplotData.js
    │   └── scatterplotStyle.js
    ├── start.js
    ├── tooltip
    │   ├── annotationView-old.js
    │   ├── index.js
    │   ├── tooltip-license.md
    │   ├── tooltip.js
    │   ├── tooltipElement.js
    │   ├── tooltipImage.js
    │   ├── tooltipLink.js
    │   ├── tooltipStyle.js
    │   ├── tooltipTable.js
    │   ├── tooltipText.js
    │   ├── tooltipView.js
    │   └── tooltipVote.js
    └── transcript
    │   ├── index.js
    │   ├── transcript.js
    │   ├── transcriptChart.js
    │   ├── transcriptData.js
    │   └── transcriptStyle.js
└── test
    └── placeholder.md


/.gitignore:
--------------------------------------------------------------------------------
1 | .DS_Store
2 | bower_components/
3 | node_modules/
4 | gd3.test.js
5 | 


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
 1 | Copyright 2013,2014,2015 Brown University, Providence, RI.
 2 | 
 3 |                          All Rights Reserved
 4 | 
 5 | Permission to use, copy, modify, and distribute this software and its
 6 | documentation for any purpose other than its incorporation into a
 7 | commercial product is hereby granted without fee, provided that the
 8 | above copyright notice appear in all copies and that both that
 9 | copyright notice and this permission notice appear in supporting
10 | documentation, and that the name of Brown University not be used in
11 | advertising or publicity pertaining to distribution of the software
12 | without specific, written prior permission.
13 | 
14 | BROWN UNIVERSITY DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
15 | INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR ANY
16 | PARTICULAR PURPOSE.  IN NO EVENT SHALL BROWN UNIVERSITY BE LIABLE FOR
17 | ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
18 | WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
19 | ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
20 | OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
21 | 


--------------------------------------------------------------------------------
/Makefile:
--------------------------------------------------------------------------------
1 | gd3.js: $(shell node_modules/.bin/smash --list src/gd3.js)
2 | 				node_modules/.bin/smash src/gd3.js | node_modules/.bin/uglifyjs - -b indent-level=2 -o $@
3 | 
4 | global: $(shell smash --list src/gd3.js)
5 | 				smash src/gd3.js | uglifyjs - -b indent-level=2 -o $@
6 | 
7 | test:	$(shell node_modules/.bin/smash --list src/gd3.js)
8 | 				node_modules/.bin/smash src/gd3.js > gd3.test.js


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | #gd3
 2 | 
 3 | A library of genomics visualizations.
 4 | 
 5 | ### Setup
 6 | 
 7 | 1. **Requirements**: [npm](https://npmjs.org/) and [node](http://nodejs.org/).
 8 | 2. **Clone**: `git clone https://<user>@bitbucket.org/raphaellab/gd3.git`.
 9 | 3. **Install dependencies**: `npm install`.
10 | 
11 | To use the Python scripts, you must also:
12 | 
13 | 1. **Clone HotNet2**: `git clone https://<user>@bitbucket.org/raphaellab/hotnet2.git`.
14 | 2. **Add "HOTNET" environment variable**: Add `setenvvar HOTNET <path/to/hotnet2/checkout>` to `~/.environment`
15 | 
16 | ### Javascript: (`js/`)
17 | 
18 | *Visualization scripts*
19 | 
20 | Mutation Matrix(`js/mutation-matrix.js`)
21 | 
22 | Subnetworks(`js/subnetwork.js`)
23 | 
24 | Transcript Plot(`js/transcript-plot.js`)
25 | 
26 | ### Styles (`js/style/`)
27 | 
28 | *Pre-defined style files.* 
29 | 
30 | `js/default-style.js`: default styles
31 | 
32 | `js/pancancer-sample-coloring.json`: cancer type -> color mapping for PanCancer
33 | 
34 | ### Draw (`.`)
35 | 
36 | *Python scripts for saving visualizations to SVG.*
37 | 
38 | Python Mutation Matrix (`drawMutationMatrix.py`)
39 | 
40 |     Usage: see python drawMutationMatrix.py -h
41 | 
42 | *Node.js scripts for saving visualizations to SVG.*
43 | 
44 | Mutation Matrix(`drawMutationMatrix.js`)
45 | 
46 |     Usage: node drawMutationMatrix.js --json=</path/to/json> --outdir=</path/to/output>
47 | 
48 | Transcript Plot(`drawTranscriptPlot.js`)
49 | 
50 |     Usage: node drawTranscriptPlot.js --json=</path/to/json> --outfile=</path/to/output/file>
51 | 


--------------------------------------------------------------------------------
/bower.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "name": "gd3",
 3 |   "version": "1.0.0",
 4 |   "homepage": "https://github.com/raphael-group/gd3",
 5 |   "authors": [
 6 |     "connor <connor@cs.brown.edu>",
 7 |     "max <mdml@cs.brown.edu>"
 8 |   ],
 9 |   "main": "gd3.js",
10 |   "license": "MIT",
11 |   "private": true,
12 |   "ignore": [
13 |     "**/.*",
14 |     "node_modules",
15 |     "bower_components",
16 |     "test",
17 |     "tests"
18 |   ],
19 |   "dependencies": {
20 |     "d3-tip": "~0.6.4",
21 |     "d3": "latest",
22 |     "jquery": "~2.1.1"
23 |   }
24 | }
25 | 


--------------------------------------------------------------------------------
/demo/test-all.html:
--------------------------------------------------------------------------------
  1 | <!DOCTYPE html>
  2 | <html class="no-js">
  3 |   <head>
  4 |     <meta charset="utf-8">
  5 |     <meta http-equiv="X-UA-Compatible" content="IE=edge">
  6 |     <title>GD3 Testing Page</title>
  7 |     <meta name="description" content="">
  8 |     <meta name="viewport" content="width=device-width, initial-scale=1">
  9 |     <style>
 10 |     hr {
 11 |       border-bottom:none;
 12 |       border-left: none;
 13 |       border-right:none;
 14 |       border-top: 1px solid #666;
 15 |     }
 16 |     </style>
 17 |   </head>
 18 |   <body>
 19 |     <div id="cna"></div>
 20 |     <hr />
 21 |     <div id="graph"></div>
 22 |     <hr />
 23 |     <div id="heatmap"></div>
 24 |     <hr />
 25 |     <div id="mutmtx"></div>
 26 |     <hr />
 27 |     <div id="transcript"></div>
 28 |     <hr/>
 29 |     <div id="dendrogram"></div>
 30 |     <div style="height:200px"></div>
 31 |     <script src="../bower_components/d3/d3.min.js"></script>
 32 |     <script src="../gd3.js"></script>
 33 |     <script>
 34 | 
 35 |     d3.json('testData/example-cna.json', function(data) {
 36 |       d3.select('#cna')
 37 |         .datum(data.PDGFRA)
 38 |         .call(gd3.cna());
 39 |     });
 40 | 
 41 |     d3.json('testData/example-graph.json', function(data) {
 42 |       var style = {
 43 |         nodeColor : ['rgb(38, 125, 255)','rgb(237, 14, 28)']
 44 |       };
 45 |         d3.select('#graph')
 46 |             .datum(data)
 47 |             .call(gd3.graph({style:style})
 48 |             );
 49 |     });
 50 | 
 51 |     d3.json('testData/example-heatmap.json', function(data) {
 52 |       d3.json('testData/exampleAnnotations.json', function(adata) {
 53 |         data.annotations = adata;
 54 |         var hStyle = {height: 260, width: 800};
 55 |         d3.select('#heatmap')
 56 |             .datum(data)
 57 |             .call(gd3.heatmap({style:hStyle}));
 58 |       });
 59 |     });
 60 | 
 61 |     d3.json('testData/example2-mutation-matrix.json', function(data) {
 62 |       d3.json('testData/exampleAnnotations.json', function(annData) {
 63 |         var mutMtxStyle = {
 64 |           width: 800
 65 |         }
 66 |         data.annotations = annData;
 67 |         d3.select('#mutmtx')
 68 |           .datum(data)
 69 |           .call(gd3.mutationMatrix({style:mutMtxStyle}));
 70 |       });
 71 |     });
 72 | 
 73 | 
 74 |     d3.json('testData/example2-transcript.json', function(data) {
 75 | 
 76 |       var styling = {
 77 |         height: 180,
 78 |         width: 345
 79 |       };
 80 | 
 81 |       var sampleTypes = {},
 82 |           params = {},
 83 |           vizData = [];
 84 | 
 85 |       params.style=styling;
 86 | 
 87 |       var categories = ['BLCA', 'BRCA', 'COADREAD', 'GBM', 'HNSC', 'LUAD', 'LUSC', 'OV', 'SCNAH'];
 88 | 
 89 |       for (gKey in Object.keys(data)) {
 90 |         var gene = Object.keys(data)[gKey],
 91 |             transcriptList = Object.keys(data[gene]);
 92 | 
 93 |         for (tKey in transcriptList) {
 94 |           var transcript = transcriptList[tKey],
 95 |               domains = data[gene][transcript].domains,
 96 |               length = data[gene][transcript].length,
 97 |               mutations = data[gene][transcript].mutations;
 98 | 
 99 |           var mKeys = Object.keys(mutations);
100 |           for(mKey in mKeys) {
101 |             var m = mKeys[mKey],
102 |                 cancer = mutations[m].cancer;
103 |             sampleTypes[cancer] = 0;
104 |           }
105 | 
106 |           vizData.push({gene: gene, transcript: transcript, domains: domains, length: length, mutations: mutations, mutationCategories: categories, proteinDomainDB: 'PFAM'});
107 |         }
108 |       }
109 |       sampleTypes = Object.keys(sampleTypes);
110 |       params.sampleTypes = sampleTypes;
111 | 
112 |       d3.select("#transcript")
113 |         .append("h3")
114 |         .html(vizData[0].gene + " <small>" + vizData[1].transcript + "</small>");
115 |       d3.select('#transcript')
116 |           .datum(vizData[0])
117 |           .call(gd3.transcript(params));
118 |     });
119 | 
120 |     d3.json('testData/example-dendrogram-N30.json', function(data) {
121 |       var hStyle = {height: 400, width: 800};
122 |       d3.select('#dendrogram')
123 |           .datum(data)
124 |           .call(gd3.dendrogram({style:hStyle}));
125 |     });
126 |     </script>
127 |   </body>
128 | </html>


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/demo/test-cna.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html class="no-js">
 3 |   <head>
 4 |     <meta charset="utf-8">
 5 |     <meta http-equiv="X-UA-Compatible" content="IE=edge">
 6 |     <title>GD3 Example CNA</title>
 7 |     <meta name="description" content="">
 8 |     <meta name="viewport" content="width=device-width, initial-scale=1">
 9 |   </head>
10 |   <body>
11 |     <table>
12 |       <tr>
13 |         <td valign="top" style='padding-right:100px'>
14 |           <h3>MYC <small>(modified to include some deletions)</small></h3>
15 |           <div id="test1"></div>
16 |         </td>
17 |         <td valign="top">
18 |           <h3>PDGFRA <small>(modified to include some deletions)</small></h3>
19 |           <div id="test2"></div>
20 |         </td>
21 |       </tr>
22 |       <tr>
23 |         <td valign="top">
24 |           <h3>PTEN</h3>
25 |           <div id="test3"></div>
26 |         </td>
27 |       </tr>
28 |     </table>
29 |     <script src="../bower_components/d3/d3.min.js"></script>
30 |     <script src="../gd3.js"></script>
31 |     <script>
32 |     d3.json('testData/example-cna.json', function(data) {
33 |       d3.select('#test1')
34 |         .datum(data.MYC)
35 |         .call(gd3.cna());
36 |       d3.select('#test2')
37 |         .datum(data.PDGFRA)
38 |         .call(gd3.cna().showScrollers(true));
39 |       d3.select('#test3')
40 |         .datum(data.PTEN)
41 |         .call(gd3.cna().showScrollers(true));
42 |     });
43 |     </script>
44 |   </body>
45 | </html>


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/demo/test-color.html:
--------------------------------------------------------------------------------
  1 | <!DOCTYPE html>
  2 | <html class="no-js">
  3 |   <head>
  4 |     <meta charset="utf-8">
  5 |     <meta http-equiv="X-UA-Compatible" content="IE=edge">
  6 |     <title>GD3 Example Color Formatting</title>
  7 |     <meta name="description" content="">
  8 |     <meta name="viewport" content="width=device-width, initial-scale=1">
  9 | <style>
 10 | * {
 11 |   font-family: "HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif;
 12 | }
 13 | </style>
 14 |   </head>
 15 |   <body>
 16 |     <script src="../bower_components/d3/d3.min.js"></script>
 17 |     <script src="../gd3.js"></script>
 18 |     <script>
 19 |       var body = d3.select('body');
 20 |       var palettes = body.append('div');
 21 |       palettes.append('h1').text('Default category palettes')
 22 |       palettes.append('p').text('The first four colors used are color blind friendly.');
 23 | 
 24 |       var data = [],
 25 |           swatchStyle = {
 26 |             display: 'inline-block',
 27 |             height: '10px',
 28 |             'margin-right': '2px',
 29 |             width: '20px'
 30 |           };
 31 | 
 32 |       for (var i = 0; i < 20; i++) {
 33 |         data.push(i);
 34 |         var palette = gd3.color.categories(data); // return the palette
 35 | 
 36 |         palette = gd3.color.categoryPalette; // or statically reference it
 37 | 
 38 |         palettes.append('div').selectAll('div')
 39 |             .data(data)
 40 |             .enter()
 41 |               .append('div')
 42 |                   .style(swatchStyle)
 43 |                   .style('background-color', function(d) { return palette(d); });
 44 | 
 45 |       }
 46 | 
 47 |       body.append('hr');
 48 | 
 49 |       body.append('p').text('D3 palettes for comparison');
 50 | 
 51 |       var tableaus = body.append('div');
 52 |       tableaus.append('div').selectAll('div')
 53 |           .data(d3.scale.category10().range())
 54 |           .enter()
 55 |             .append('div')
 56 |                 .style(swatchStyle)
 57 |                 .style('background-color', function(d) { return d; });
 58 |       tableaus.append('div').selectAll('div')
 59 |           .data(d3.scale.category20().range())
 60 |           .enter()
 61 |             .append('div')
 62 |                 .style(swatchStyle)
 63 |                 .style('background-color', function(d) { return d; });
 64 | 
 65 |       body.append('hr');
 66 | 
 67 |       //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 68 | 
 69 |       body.append('h1').text('Default annotation palettes');
 70 | 
 71 |       body.append('p').text('Discrete annotation palettes');
 72 | 
 73 |       body.append('div').selectAll('div')
 74 |           .data(gd3.color.palettes.annotation_discrete)
 75 |           .enter()
 76 |           .append('div')
 77 |           .selectAll('div')
 78 |               .data(function(d) { return d; })
 79 |               .enter()
 80 |               .append('div')
 81 |                   .style(swatchStyle)
 82 |                   .style('background-color', function(d) { return d; });
 83 | 
 84 |       body.append('p').text('Continuous annotation palettes');
 85 | 
 86 |       body.append('div').selectAll('div')
 87 |           .data(gd3.color.palettes.annotation_continuous)
 88 |           .enter()
 89 |           .append('div')
 90 |           .selectAll('div')
 91 |               .data(function(d) { return d; })
 92 |               .enter()
 93 |               .append('div')
 94 |                   .style(swatchStyle)
 95 |                   .style('background-color', function(d) { return d; });
 96 | 
 97 |       //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 98 | 
 99 |       body.append('h2').text('For mutation matrix examples, try sorting by category');
100 |       body.append('p').text('Mutation matrix with default coloring, no categories specified');
101 |       var m1 = body.append('div');
102 |       body.append('br').append('br');
103 |       body.append('p').text('Mutation matrix with its categories added');
104 |       var m2 = body.append('div');
105 |       body.append('br').append('br');
106 |       body.append('p').text('Mutation matrix with its categories added and some additional ones');
107 |       var m3 = body.append('div');
108 |       body.append('hr');
109 |       var t1 = body.append('div');
110 |       body.append('hr');
111 |       var cna1 = body.append('div');
112 |       body.append('br');
113 |       var cna2 = body.append('div');
114 | 
115 |       // clear the palette information for the next example
116 |       gd3.color.categoryPalette = undefined;
117 | 
118 |       var mutmtxStyle = {
119 |         width: 800
120 |       }
121 | 
122 |       d3.json('testData/example2-mutation-matrix.json', function(data) {
123 |         d3.json('testData/exampleAnnotations.json', function(annData) {
124 | 
125 |           data.annotations = annData;
126 | 
127 |           m1.datum(data)
128 |             .call(gd3.mutationMatrix({style:mutmtxStyle}));
129 | 
130 |           var categories = ['BLCA', 'BRCA', 'COADREAD', 'GBM','HNSC','KIRC','LAML','LUAD','LUSC','OV','UCEC'];
131 |           gd3.color.categories(categories);
132 | 
133 |           m2.datum(data)
134 |             .call(gd3.mutationMatrix({style:mutmtxStyle}));
135 | 
136 |           var categories = [1,2,'BLCA', 'BRCA', 'COADREAD', 'GBM','HNSC','KIRC','LAML','LUAD','LUSC','OV','UCEC'];
137 |           gd3.color.categories(categories);
138 | 
139 |           m3.datum(data)
140 |             .call(gd3.mutationMatrix({style:mutmtxStyle}));
141 |         });
142 |       });
143 | 
144 |       // Render the transcripts and see if the color is the same.
145 | 
146 |       d3.json('testData/example2-transcript.json', function(data) {
147 |         var styling = {
148 |           height: 180,
149 |           width: 345
150 |         };
151 | 
152 |         var sampleTypes = {}, params = {}, vizData = [];
153 |         params.style=styling;
154 | 
155 |         var categories = ['BLCA', 'BRCA', 'COADREAD', 'GBM', 'HNSC', 'LUAD', 'LUSC', 'OV', 'SCNAH'];
156 | 
157 |         for (gKey in Object.keys(data)) {
158 |           var gene = Object.keys(data)[gKey], transcriptList = Object.keys(data[gene]);
159 | 
160 |           for (tKey in transcriptList) {
161 |             var transcript = transcriptList[tKey], domains = data[gene][transcript].domains, length = data[gene][transcript].length, mutations = data[gene][transcript].mutations;
162 | 
163 |             var mKeys = Object.keys(mutations);
164 |             for(mKey in mKeys) {
165 |               var m = mKeys[mKey], cancer = mutations[m].cancer;
166 |               sampleTypes[cancer] = 0;
167 |             }
168 | 
169 |             vizData.push({gene: gene, transcript: transcript, domains: domains, length: length, mutations: mutations, mutationCategories: categories, proteinDomainDB: 'PFAM'});
170 |           }
171 |         }
172 |         sampleTypes = Object.keys(sampleTypes);
173 |         params.sampleTypes = sampleTypes;
174 | 
175 |         // Update color categories
176 |         var categories = [1,2,'BLCA', 'BRCA', 'COADREAD', 'GBM','HNSC','KIRC','LAML','LUAD','LUSC','OV','UCEC'];
177 |         gd3.color.categories(categories);
178 | 
179 |         // Draw STAG1 where no scrollbar should appear
180 |         t1.datum(vizData[0])
181 |             .call(gd3.transcript(params));
182 | 
183 |         // Draw BRAF where an activating (top) scrollbar should appear
184 |         d3.select('#test2')
185 |           .append('h3')
186 |           .html(vizData[1].gene + " <small>" + vizData[1].transcript + "</small>");
187 |         d3.select('#test2')
188 |             .datum(vizData[1])
189 |             .call(gd3.transcript(params));
190 | 
191 |         // Draw ARID1A where both inactivating (bottom) and activating (top)
192 |         // scrollbars should appear
193 |         d3.select('#test3')
194 |           .append('h3')
195 |           .html(vizData[2].gene + " <small>" + vizData[2].transcript + "</small>");
196 |         d3.select('#test3')
197 |             .datum(vizData[2])
198 |             .call(gd3.transcript(params));
199 |       });
200 | 
201 |       d3.json('testData/example-cna.json', function(data) {
202 |         cna2.datum(data.PDGFRA)
203 |           .call(gd3.cna());
204 |       });
205 | 
206 |       //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
207 |       // Test annoatation coloring
208 |       body.append('hr');
209 |       body.append('hr');
210 | 
211 |       var mutmtxA = body.append('div'),
212 |           aBreak = body.append('br').append('br'),
213 |           hmapA = body.append('div');
214 | 
215 |       d3.json('testData/exampleAnnotations.json', function(annData) {
216 | 
217 |         gd3.color.annotations('Gender', ['female', 'male'], 'discrete', ['#ff0000', '#0000ff']);
218 | 
219 |         var values = Object.keys(annData.sampleToAnnotations).map(function(key) {
220 |               return annData.sampleToAnnotations[key][0];
221 |             });
222 |         values = d3.set(values).values().map(function(d) { return + d; });
223 |         gd3.color.annotations('Survival (days)', [d3.min(values), d3.max(values)], 'continuous', ['#88ff88', '#000000']);
224 | 
225 |         d3.json('testData/example2-mutation-matrix.json', function(data) {
226 |           data.annotations = annData;
227 | 
228 |           var categories = ['BLCA', 'BRCA', 'COADREAD', 'GBM','HNSC','KIRC','LAML','LUAD','LUSC','OV','UCEC'];
229 |           gd3.color.categories(categories);
230 | 
231 |           mutmtxA.datum(data)
232 |             .call(gd3.mutationMatrix({style:mutmtxStyle}));
233 |         });
234 | 
235 |         d3.json('testData/example-heatmap.json', function(data) {
236 |           data.annotations = annData;
237 |           var hStyle = {width: 800};
238 |           hmapA.datum(data)
239 |               .call(gd3.heatmap({style:hStyle}));
240 |         });
241 |       });
242 |     </script>
243 |   </body>
244 | </html>


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/demo/test-dendrogram.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html class="no-js">
 3 |   <head>
 4 |     <meta charset="utf-8">
 5 |     <meta http-equiv="X-UA-Compatible" content="IE=edge">
 6 |     <title>GD3 Example Transcript Annotation</title>
 7 |     <meta name="description" content="">
 8 |     <meta name="viewport" content="width=device-width, initial-scale=1">
 9 |   </head>
10 |   <body>
11 |     <div id="dendrogram"></div>
12 |     <script src="../bower_components/d3/d3.min.js"></script>
13 |     <script src="../gd3.js"></script>
14 |     <script>
15 |     d3.json('testData/example-dendrogram-N30.json', function(data) {
16 |       var hStyle = {height: 600, width: 1200};
17 |       d3.select('#dendrogram')
18 |           .datum(data)
19 |           .call(gd3.dendrogram({style:hStyle}).showSlider().logScale(false));
20 |     });
21 |     </script>
22 |   </body>
23 | </html>


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/demo/test-dispatch.html:
--------------------------------------------------------------------------------
  1 | <!DOCTYPE html>
  2 | <html class="no-js">
  3 |   <head>
  4 |     <meta charset="utf-8">
  5 |     <meta http-equiv="X-UA-Compatible" content="IE=edge">
  6 |     <title>GD3 Example Linking of Views with Dispatch</title>
  7 |     <meta name="description" content="">
  8 |     <meta name="viewport" content="width=device-width, initial-scale=1">
  9 |     <style>
 10 | 
 11 | * {
 12 |   font-family: "HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif;
 13 | }
 14 | 
 15 | a {
 16 |   color: steelblue;
 17 | }
 18 | a:visited {
 19 |   color: steelblue;
 20 | }
 21 | 
 22 |     </style>
 23 |   </head>
 24 |   <body>
 25 |     <h2>Sample linking</h2>
 26 |     <div id="samples"></div>
 27 |     <hr/>
 28 |     <h2>Form update</h2>
 29 |     <div id="form-linking">
 30 |       <form style='float:right;margin-right:40%'>
 31 |         <b>Form</b><br/><br/>
 32 |         <select id="protein1"><option>--choose protein--</option></select>
 33 |         <br/><br/>
 34 |         <select id="protein2"><option>--choose protein--</option></select>
 35 |         <br/><br/>
 36 |         <input id="pmid" placeholder="PMID">
 37 |         <br/><br/>
 38 |         <textarea id="comments" placeholder="Enter any comments"></textarea>
 39 |       </form>
 40 |     </div>
 41 |     <script src="../bower_components/d3/d3.min.js"></script>
 42 |     <script src="../gd3.js"></script>
 43 |     <script>
 44 |     var body = d3.select('#samples');
 45 |     var style = {
 46 |       width: 800
 47 |     }
 48 | 
 49 |     // Add the mutation matrix
 50 |     var mutmtx = body.append('div').attr('id', 'mutmtxtest');
 51 |     d3.json('testData/example2-mutation-matrix.json', function(mutData) {
 52 |       d3.json('testData/exampleAnnotations.json', function(annData) {
 53 |         mutData.annotations = annData;
 54 |         body.append("h3").text("Mutation matrix")
 55 |         body.append('div').attr('id', '#mutmtxtest')
 56 |           .datum(mutData)
 57 |           .call(gd3.mutationMatrix({style:style}));
 58 |         var sampleNames = mutData.samples.map(function(d){ return d.name; })
 59 | 
 60 |         // Add the transcript plot
 61 |         d3.json('testData/example2-transcript.json', function(data) {
 62 | 
 63 |           var styling = {
 64 |             height: 180,
 65 |             width: 345
 66 |           };
 67 | 
 68 |           var sampleTypes = {},
 69 |               params = {},
 70 |               vizData = [];
 71 | 
 72 |           params.style=styling;
 73 | 
 74 |           var categories = ['BLCA', 'BRCA', 'COADREAD', 'GBM', 'HNSC', 'LUAD', 'LUSC', 'OV', 'SCNAH'];
 75 |           for (gKey in Object.keys(data)) {
 76 |             var gene = Object.keys(data)[gKey],
 77 |                 transcriptList = Object.keys(data[gene]);
 78 | 
 79 |             for (tKey in transcriptList) {
 80 |               var transcript = transcriptList[tKey],
 81 |                   domains = data[gene][transcript].domains,
 82 |                   length = data[gene][transcript].length,
 83 |                   mutations = data[gene][transcript].mutations;
 84 | 
 85 |               var mKeys = Object.keys(mutations);
 86 |               for(mKey in mKeys) {
 87 |                 var m = mKeys[mKey],
 88 |                     cancer = mutations[m].cancer;
 89 |                 sampleTypes[cancer] = 0;
 90 |               }
 91 | 
 92 |               vizData.push({gene: gene, transcript: transcript, domains: domains, length: length, mutations: mutations, mutationCategories: categories, proteinDomainDB: 'PFAM'});
 93 | 
 94 |             }
 95 |           }
 96 |           sampleTypes = Object.keys(sampleTypes);
 97 |           params.sampleTypes = sampleTypes;
 98 | 
 99 | 
100 |         body.append("h3").text("Transcript plot")
101 |           body.append("div")
102 |               .datum(vizData[0])
103 |               .call(gd3.transcript(params));
104 | 
105 | 
106 |             d3.json('testData/example-cna.json', function(data) {
107 |               body.append("h3").text("CNA browser");
108 |               body.append("div")
109 |                 .datum(data.PDGFRA)
110 |                 .call(gd3.cna());
111 |             });
112 |         });
113 | 
114 |       });
115 |     });
116 | 
117 |     d3.json('testData/example-graph.json', function(data) {
118 |         var style = {
119 |           nodeColor : ['rgb(38, 125, 255)','rgb(237, 14, 28)']
120 |         };
121 |         d3.select('#form-linking')
122 |             .datum(data)
123 |             .call(gd3.graph({style:style}));
124 | 
125 |         d3.selectAll("select")
126 |           .selectAll(".option")
127 |           .data(data.nodes).enter()
128 |           .append("option")
129 |           .attr('value', function(d){ return d.name; })
130 |           .text(function(d){ return d.name; });
131 |     });
132 | 
133 |     gd3.dispatch.on("interaction.graph", function(d){
134 |       d3.select("select#protein1").property('value', d.source);
135 |       d3.select("select#protein2").property('value', d.target);
136 |     });
137 | 
138 | 
139 |     body.append('hr');
140 |     body.append('h1').text('Filtering dispatch test');
141 |     var filterCategoryMenu = body.append('div').style('margin-bottom', '50px'),
142 |         filterTypeMenu = body.append('div'),
143 |         breaker = body.append('br').append('br').append('hr');
144 | 
145 |     var categories = [
146 |         'STAD',
147 |         'BLCA',
148 |         'BRCA',
149 |         'COADREAD',
150 |         'GBM',
151 |         'HNSC',
152 |         'KIRC',
153 |         'LAML',
154 |         'LUAD',
155 |         'LUSC',
156 |         'OV',
157 |         'UCEC'
158 |     ];
159 |     var filterCategoryMenuText = filterCategoryMenu.selectAll('span')
160 |         .data(categories)
161 |         .enter()
162 |         .append('span')
163 |             .style('border', '1px solid #ccc')
164 |             .style('font-size', '14px')
165 |             .style('padding', '10px')
166 |             .text(function(d){return d;});
167 |     filterCategoryMenuInput = filterCategoryMenuText.append('input')
168 |         .attr('type', 'checkbox')
169 |         .on('click', applyCategoryFilter);
170 | 
171 |     function applyCategoryFilter() {
172 |       var checked = filterCategoryMenuInput.filter(function(d) {
173 |         return d3.select(this).property('checked');
174 |       });
175 | 
176 |       var filtering = [];
177 |       checked.each(function(d) { filtering.push(d); });
178 |       gd3.dispatch.filterCategory( {categories: filtering });
179 |     }
180 | 
181 |     var types = ['snv', 'inactive_snv'];
182 |     var filterTypeMenuText = filterTypeMenu.selectAll('span')
183 |         .data(types)
184 |         .enter()
185 |         .append('span')
186 |             .style('border', '1px solid #ccc')
187 |             .style('font-size', '14px')
188 |             .style('padding', '10px')
189 |             .text(function(d){return d;});
190 |     filterTypeMenuInput = filterTypeMenuText.append('input')
191 |         .attr('type', 'checkbox')
192 |         .on('click', applyTypeFilter);
193 | 
194 |     function applyTypeFilter() {
195 |       var checked = filterTypeMenuInput.filter(function(d) {
196 |         return d3.select(this).property('checked');
197 |       });
198 | 
199 |       var filtering = [];
200 |       checked.each(function(d) { filtering.push(d); });
201 |       gd3.dispatch.filterType( { types: filtering });
202 |     }
203 | 
204 | 
205 |     body.append('hr');
206 |     body.append('h1').text('Sorting dispatch test');
207 |     var sortMutMtx = body.append('div'),
208 |         breaker = body.append('br').append('br'),
209 |         sortHeatmap = body.append('div');
210 | 
211 |     d3.json('testData/example2-mutation-matrix.json', function(data) {
212 |       d3.json('testData/exampleAnnotations.json', function(annData) {
213 |         data.annotations = annData;
214 |         sortMutMtx.datum(data).call(gd3.mutationMatrix({style:style}));
215 |       });
216 |     });
217 |     d3.json('testData/example-heatmap.json', function(data) {
218 |       d3.json('testData/exampleAnnotations.json', function(adata) {
219 |         data.annotations = adata;
220 |         var hStyle = {height: 260, width: 800};
221 |         sortHeatmap.datum(data).call(gd3.heatmap({style:hStyle}));
222 |       });
223 |     });
224 | 
225 |     body.append('hr');
226 | 
227 | 
228 |     </script>
229 |   </body>
230 | </html>


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/demo/test-graph.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html class="no-js">
 3 |   <head>
 4 |     <meta charset="utf-8">
 5 |     <meta http-equiv="X-UA-Compatible" content="IE=edge">
 6 |     <title>GD3 Example Transcript Annotation</title>
 7 |     <meta name="description" content="">
 8 |     <meta name="viewport" content="width=device-width, initial-scale=1">
 9 |   </head>
10 |   <body>
11 |     <div id="test"></div>
12 |     <script src="../bower_components/d3/d3.min.js"></script>
13 |     <script src="../gd3.js"></script>
14 |     <script>
15 | 
16 |     d3.json('testData/example-graph.json', function(data) {
17 |       var style = {
18 |         nodeColor : ['rgb(38, 125, 255)','rgb(237, 14, 28)']
19 |       };
20 |         d3.select('#test')
21 |             .datum(data)
22 |             .call(gd3.graph({style:style})
23 |             );
24 |     });
25 |     </script>
26 |   </body>
27 | </html>


--------------------------------------------------------------------------------
/demo/test-heatmap.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html class="no-js">
 3 |   <head>
 4 |     <meta charset="utf-8">
 5 |     <meta http-equiv="X-UA-Compatible" content="IE=edge">
 6 |     <title>GD3 Example Transcript Annotation</title>
 7 |     <meta name="description" content="">
 8 |     <meta name="viewport" content="width=device-width, initial-scale=1">
 9 |   </head>
10 |   <body>
11 |     <div id="heatmap"></div>
12 |     <script src="../bower_components/d3/d3.min.js"></script>
13 |     <script src="../gd3.js"></script>
14 |     <script>
15 |     d3.json('testData/example-heatmap.json', function(data) {
16 |       d3.json('testData/exampleAnnotations.json', function(adata) {
17 |         data.annotations = adata;
18 |         var hStyle = {width: 800};
19 |         d3.select('#heatmap')
20 |             .datum(data)
21 |             .call(gd3.heatmap({style:hStyle}));
22 |       });
23 |     });
24 |     </script>
25 |   </body>
26 | </html>


--------------------------------------------------------------------------------
/demo/test-mutmtx.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html class="no-js">
 3 |   <head>
 4 |     <meta charset="utf-8">
 5 |     <meta http-equiv="X-UA-Compatible" content="IE=edge">
 6 |     <title>GD3 Example Mutation Matrix</title>
 7 |     <meta name="description" content="">
 8 |     <meta name="viewport" content="width=device-width, initial-scale=1">
 9 |   </head>
10 |   <body>
11 |     <div id="test"></div>
12 |     <script src="../bower_components/d3/d3.min.js"></script>
13 |     <script src="../gd3.js"></script>
14 |     <script>
15 | 
16 |     var style = {
17 |       width: 800
18 |     }
19 | 
20 |     d3.json('testData/example2-mutation-matrix.json', function(data) {
21 |       d3.select('#test')
22 |         .datum(data)
23 |         .call(gd3.mutationMatrix({style:style}));
24 |     });
25 |     </script>
26 |   </body>
27 | </html>


--------------------------------------------------------------------------------
/demo/test-scatterplot.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html class="no-js">
 3 |   <head>
 4 |     <meta charset="utf-8">
 5 |     <meta http-equiv="X-UA-Compatible" content="IE=edge">
 6 |     <title>GD3 Example Scatterplot</title>
 7 |     <meta name="description" content="">
 8 |     <meta name="viewport" content="width=device-width, initial-scale=1">
 9 |   </head>
10 |   <body>
11 |     <div id="test"></div>
12 |     <script src="../bower_components/d3/d3.min.js"></script>
13 |     <script src="../gd3.js"></script>
14 |     <script>
15 | 
16 |     d3.json('testData/example-scatterplot.json', function(data) {
17 |       var style = {
18 |         margins : { bottom: 50, left: 35, right: 60, top: 14},
19 |         width: 350
20 |       }
21 |       d3.select('#test')
22 |           .datum(data)
23 |           .call(gd3.scatterplot({style:style}));
24 |     });
25 |     </script>
26 |   </body>
27 | </html>


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/demo/test-tooltip.html:
--------------------------------------------------------------------------------
  1 | <!DOCTYPE html>
  2 | <html class="no-js">
  3 |   <head>
  4 |     <meta charset="utf-8">
  5 |     <meta http-equiv="X-UA-Compatible" content="IE=edge">
  6 |     <title>GD3 Example Mutation Matrix</title>
  7 |     <meta name="description" content="">
  8 |     <meta name="viewport" content="width=device-width, initial-scale=1">
  9 |     <style>
 10 | 
 11 | a {
 12 |   color: steelblue;
 13 | }
 14 | a:visited {
 15 |   color: steelblue;
 16 | }
 17 | 
 18 |     </style>
 19 |   </head>
 20 |   <body>
 21 |     <div id="test"></div>
 22 |     <script src="../bower_components/d3/d3.min.js"></script>
 23 |     <script src="../gd3.js"></script>
 24 |     <script>
 25 | 
 26 |     function testDownvote(d) {
 27 |       console.log('voted down');
 28 |     }
 29 |     function testUpvote(d) {
 30 |       console.log('voted up');
 31 |     }
 32 |     function testDownvoteVariant(d) {
 33 |       console.log('voted down 2');
 34 |     }
 35 |     function testUpvoteVariant(d) {
 36 |       console.log('voted up 2');
 37 |     }
 38 | 
 39 |     var body = d3.select('body');
 40 | 
 41 |     var style = {
 42 |       width: 800
 43 |     }
 44 | 
 45 |     var svg = body.append('svg')
 46 |         .style('margin-left', '50px')
 47 |         .style('margin-top', '50px')
 48 |         .attr('width', 100)
 49 |         .attr('height', 40);
 50 |     svg.append('rect')
 51 |         .attr('width', 40)
 52 |         .attr('height', 40)
 53 |         .attr('class', 'gd3-tipobj')
 54 |         .style('fill', 'steelblue');
 55 | 
 56 |     svg.append('rect')
 57 |         .attr('x', 50)
 58 |         .attr('width', 40)
 59 |         .attr('height', 40)
 60 |         .attr('class', 'gd3-tipobj')
 61 |         .style('fill', 'orange');
 62 | 
 63 |     svg.call(gd3.tooltip.make().html(function(d,i) { return '<span>'+i+'</span>'; }));
 64 | 
 65 |     body.append('br');
 66 | 
 67 |     var svgdos = body.append('svg')
 68 |         .style('margin-left', '50px')
 69 |         .style('margin-top', '50px')
 70 |         .attr('width', 20)
 71 |         .attr('height', 20);
 72 |     svgdos.append('rect')
 73 |         .attr('width', 20)
 74 |         .attr('height', 20)
 75 |         .attr('class', 'gd3-tipobj')
 76 |         .style('fill', 'crimson');
 77 | 
 78 |     svgdos.call(gd3.tooltip.make().html(function(d) { return '<span>hola</span>'; }));
 79 | 
 80 |     body.append('br');
 81 | 
 82 |     body.append('hr');
 83 | 
 84 |     var testText = new gd3.tooltip.text('Testing tooltip\n'),
 85 |         imgSrc = 'https://www.google.com/images/srpr/logo11w.png',
 86 |         testImg = new gd3.tooltip.image(imgSrc, 'Google\'s logo'),
 87 |         testLink = new gd3.tooltip.link('https://google.com', 'Google Link\n'),
 88 |         testLinkImg = new gd3.tooltip.link('https://google.com', testImg),
 89 |         testVote = new gd3.tooltip.vote(testDownvote,testUpvote,d3.functor(80));
 90 | 
 91 |     testText.render(body);
 92 |     body.append('br');
 93 |     testLink.render(body);
 94 |     body.append('br');
 95 |     testLinkImg.render(body);
 96 |     body.append('br');
 97 |     testImg.render(body);
 98 |     body.append('br');
 99 |     testVote.render(body);
100 | 
101 |     var testTable = new gd3.tooltip.table([ [1,2,3], [4,5,testText] ] );
102 |     testTable.render(body);
103 | 
104 |     body.append('br');
105 | 
106 |     var testDatum = gd3.tooltip.datum({type: 'text', text:'datum text test works' });
107 |     testDatum.render(body);
108 | 
109 |     body.append('br');
110 |     body.append('hr');
111 | 
112 |     var svgtres = body.append('svg')
113 |         .style('margin-bottom', '20px')
114 |         .style('margin-left', '50px')
115 |         .style('margin-top', '50px')
116 |         .attr('width', 50)
117 |         .attr('height', 20);
118 |     svgtres.append('rect')
119 |         .attr('width', 20)
120 |         .attr('height', 20)
121 |         .attr('class', 'gd3-tipobj')
122 |         .style('fill', 'steelblue');
123 |     svgtres.append('circle')
124 |             .attr('cx', 35)
125 |             .attr('cy',10)
126 |             .attr('r', 10)
127 |             .attr('class', 'gd3-tipobj')
128 |             .style('fill', 'crimson');
129 | 
130 |     var testingData = [
131 |           [{ type: 'text', text: 'The title would go here.'},
132 |             { type: 'link', href: 'https://google.com', body: 'Google link test'}
133 |           ].map(gd3.tooltip.datum),
134 |           [{ type: 'text', text: 'El título estaría aquí.'},
135 |             { type: 'link', href: 'https://google.com', body: 'Google link test'}
136 |           ].map(gd3.tooltip.datum)
137 |         ];
138 | 
139 |     // need to figure out how to call this array intelligently with the tooltip
140 |     svgtres.call(gd3.tooltip.make().useData(testingData));
141 | 
142 |     body.append('br');
143 |     body.append('hr');
144 | 
145 |     var svg_groupTest = body.append('svg')
146 |         .style('background', '#ccc')
147 |         .style('margin-bottom', '20px')
148 |         .style('margin-left', '50px')
149 |         .style('margin-top', '50px')
150 |         .attr('width', 100)
151 |         .attr('height', 100);
152 | 
153 |     var groupTest_g = svg_groupTest.selectAll('g')
154 |         .data(['rect','circle'])
155 |         .enter()
156 |         .append('g')
157 |             .attr('class', 'gd3-tipobj')
158 |             .style('pointer-events', 'all');
159 | 
160 |     groupTest_g.each(function(d,i) {
161 |       var g = d3.select(this),
162 |           elems = g.selectAll(d).data([1,2]).enter().append(d);
163 | 
164 |       if(d == 'rect') {
165 |         elems.attr('height', 20)
166 |             .attr('width', 20)
167 |             .attr('x', function(el,j) { return j*25 + 10; })
168 |             .attr('y', i*25 + 10)
169 |             .style('fill', 'crimson');
170 |       } else { // is circle
171 |         elems.attr('cx', function(el,j) { return j*25 + 20; })
172 |             .attr('cy', i*25 + 20)
173 |             .attr('r', 10)
174 |             .style('fill', 'steelblue');
175 |       }
176 |     });
177 | 
178 |     svg_groupTest.call(gd3.tooltip.make().useData(testingData));
179 | 
180 |     body.append('br');
181 |     body.append('hr');
182 | 
183 |     var mutmtx = body.append('div').attr('id', 'mutmtxtest');
184 | 
185 |     d3.json('testData/example2-mutation-matrix.json', function(data) {
186 |       d3.json('testData/exampleAnnotations.json', function(annData) {
187 |         data.annotations = annData;
188 |         d3.select('#mutmtxtest')
189 |           .datum(data)
190 |           .call(gd3.mutationMatrix({style:style}));
191 | 
192 |         var cols = mutmtx.selectAll('.mutmtxColumn');
193 |         cols.classed('gd3-tipobj', true);
194 | 
195 |         var testMutmtxData = [];
196 |         cols.each(function(d,i) {
197 |           testMutmtxData.push([
198 |             { type: 'table', table: [ [ 1, 2, 3 ], [ 4, 5, 6], [testImg] ]},
199 |             { type: 'text', text: 'Number ' + i },
200 |             { type: 'vote', downvoteFn: testDownvote, upvoteFn: testUpvote, voteCountFn: d3.functor(111) }
201 |           ].map(gd3.tooltip.datum) );
202 |         });
203 | 
204 |         mutmtx.select('svg').call(gd3.tooltip.make().useData(testMutmtxData));
205 |       });
206 |     });
207 | 
208 |     body.append('br');
209 |     body.append('hr');
210 | 
211 |     body.append('p').text('Test show-on-click functionality for tooltips');
212 | 
213 |     var svg_hideTest = body.append('svg').style('margin-left', '100px');
214 | 
215 |     svg_hideTest.append('rect')
216 |         .attr('width', 20)
217 |         .attr('height', 20)
218 |         .attr('class', 'gd3-tipobj')
219 |         .style('fill', 'steelblue');
220 |     svg_hideTest.append('circle')
221 |             .attr('cx', 35)
222 |             .attr('cy',10)
223 |             .attr('r', 10)
224 |             .attr('class', 'gd3-tipobj')
225 |             .style('fill', 'crimson');
226 | 
227 |     var hiddenData = [
228 |           [{ type: 'text', text: 'The title would go here.'},
229 |             { type: 'text', text: 'More text.'},
230 |             { type: 'link', href: 'https://google.com', body: 'Google link test'},
231 |             { type: 'vote', downvoteFn: testDownvoteVariant, upvoteFn: testUpvoteVariant, voteCountFn: d3.functor(0) },
232 |             { type: 'text', text: 'Hidden text', defaultHidden: true },
233 |             { type: 'text', text: 'Not hidden text', defaultHidden: false },
234 |             { type: 'text', text: 'Even more hidden text', defaultHidden: true }
235 |           ].map(gd3.tooltip.datum),
236 |           [{ type: 'text', text: 'El título estaría aquí.'},
237 |             { type: 'link', href: 'https://google.com', body: 'Google link test'},
238 |             { type: 'text', text: 'Texto escondido', defaultHidden: true }
239 |           ].map(gd3.tooltip.datum)
240 |         ];
241 | 
242 |     svg_hideTest.call(gd3.tooltip.make().useData(hiddenData));
243 | 
244 |     </script>
245 |   </body>
246 | </html>


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/demo/test-transcript.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html class="no-js">
 3 |   <head>
 4 |     <meta charset="utf-8">
 5 |     <meta http-equiv="X-UA-Compatible" content="IE=edge">
 6 |     <title>GD3 Example Transcript Annotation</title>
 7 |     <meta name="description" content="">
 8 |     <meta name="viewport" content="width=device-width, initial-scale=1">
 9 |   </head>
10 |   <body>
11 |     <div id="test1">
12 |       <b>Select protein domain database for first transcript plot</b><br/>
13 |       <input type="radio" name="domain" value="CD"> CD
14 |       <br/>
15 |       <input type="radio" name="domain" value="PFAM" checked="checked"> PFAM
16 |       <br/>
17 |       <input type="radio" name="domain" value="SMART"> SMART
18 |     </div>
19 |     <div id="test2"></div>
20 |     <div id="test3"></div>
21 |     <script src="../bower_components/d3/d3.min.js"></script>
22 |     <script src="../bower_components/jquery/dist/jquery.min.js"></script>
23 |     <script src="../gd3.js"></script>
24 |     <script>
25 |     d3.json('testData/example3-transcript.json', function(data) {
26 |       var styling = {
27 |         height: 180,
28 |         width: 345
29 |       };
30 | 
31 |       var sampleTypes = {},
32 |           params = {showScrollers: false},
33 |           vizData = [];
34 | 
35 |       params.style=styling;
36 | 
37 |       var categories = ['BLCA', 'BRCA', 'COADREAD', 'GBM', 'HNSC', 'LUAD', 'LUSC', 'OV', 'SCNAH'];
38 | 
39 |       for (gKey in Object.keys(data)) {
40 |         var gene = Object.keys(data)[gKey],
41 |             transcriptList = Object.keys(data[gene]);
42 | 
43 |         for (tKey in transcriptList) {
44 |           var transcript = transcriptList[tKey],
45 |               domains = data[gene][transcript].domains,
46 |               length = data[gene][transcript].length,
47 |               mutations = data[gene][transcript].mutations,
48 |               sequence = data[gene][transcript].protein_sequence,
49 |               sequence_annotations = data[gene][transcript].sequence_annotations;
50 |           var mKeys = Object.keys(mutations);
51 |           for(mKey in mKeys) {
52 |             var m = mKeys[mKey],
53 |                 cancer = mutations[m].cancer;
54 |             sampleTypes[cancer] = 0;
55 |           }
56 | 
57 |           vizData.push({gene: gene, transcript: transcript, domains: domains, length: length, mutations: mutations, mutationCategories: categories, protein_sequence: sequence, sequence_annotations: sequence_annotations, proteinDomainDB: 'PFAM'});
58 |         }
59 |       }
60 |       sampleTypes = Object.keys(sampleTypes);
61 |       params.sampleTypes = sampleTypes;
62 | 
63 |       // Draw STAG1 where no scrollbar should appear
64 |       var transcriptFn = gd3.transcript(params);
65 |       d3.select('#test1')
66 |         .append('h3')
67 |         .html(vizData[0].gene + " <small>" + vizData[0].transcript + "</small>");
68 |       d3.select('#test1')
69 |           .datum(vizData[0])
70 |           .call(transcriptFn);
71 | 
72 |       $('#test1 input').click(function(){
73 |         if ($(this).is(':checked')){
74 |           transcriptFn.setDomainDB($(this).val());
75 |         }
76 |       });
77 | 
78 |       // Draw BRAF where an activating (top) scrollbar should appear
79 |       d3.select('#test2')
80 |         .append('h3')
81 |         .html(vizData[1].gene + " <small>" + vizData[1].transcript + "</small>");
82 |       d3.select('#test2')
83 |           .datum(vizData[1])
84 |           .call(gd3.transcript(params));
85 | 
86 |       // Draw ARID1A where both inactivating (bottom) and activating (top)
87 |       // scrollbars should appear
88 |       d3.select('#test3')
89 |         .append('h3')
90 |         .html(vizData[2].gene + " <small>" + vizData[2].transcript + "</small>");
91 |       d3.select('#test3')
92 |           .datum(vizData[2])
93 |           .call(gd3.transcript(params));
94 |     });
95 |     </script>
96 |   </body>
97 | </html>
98 | 


--------------------------------------------------------------------------------
/demo/testData/example-annotation.json:
--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
/demo/testData/extractAnnotationfromwhole.py:
--------------------------------------------------------------------------------
 1 | import json
 2 | 
 3 | with open('entireJson.json') as dataFile:
 4 |   data = json.load(dataFile)
 5 | 
 6 | print data.keys()
 7 | 
 8 | antData = data['annotations']
 9 | with open('example-annotation.json', 'w') as outfile:
10 |   json.dump(antData, outfile)


--------------------------------------------------------------------------------
/demo/testData/extractCNAfromwhole.py:
--------------------------------------------------------------------------------
1 | import json
2 | 
3 | with open('entireJson.json') as dataFile:
4 |   data = json.load(dataFile)
5 | 
6 | cnaData = data['cna_browser_data']
7 | with open('example-cna.json', 'w') as outfile:
8 |   json.dump(cnaData, outfile)


--------------------------------------------------------------------------------
/demo/testData/extractMutMtxfromwhole.py:
--------------------------------------------------------------------------------
 1 | import json
 2 | 
 3 | with open('entireJson.json') as dataFile:
 4 |   data = json.load(dataFile)
 5 | 
 6 | print data.keys()
 7 | 
 8 | mtxData = data['mutation_matrix']
 9 | with open('example2-mutation-matrix.json', 'w') as outfile:
10 |   json.dump(mtxData, outfile)


--------------------------------------------------------------------------------
/demo/testData/extractTranscriptfromwhole.py:
--------------------------------------------------------------------------------
1 | import json
2 | 
3 | with open('entireJson.json') as dataFile:
4 |   data = json.load(dataFile)
5 | 
6 | tData = data['transcript_data']
7 | with open('example2-transcript.json', 'w') as outfile:
8 |   json.dump(tData, outfile)


--------------------------------------------------------------------------------
/package.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "name": "gd3prime",
 3 |   "version": "1.0.0",
 4 |   "description": "",
 5 |   "main": "gd3.js",
 6 |   "dependencies": {
 7 |     "uglify-js": "~2.4.15",
 8 |     "smash": "~0.0.12",
 9 |     "bower": "latest"
10 |   },
11 |   "devDependencies": {},
12 |   "scripts": {
13 |     "test": "echo \"Error: no test specified\" && exit 1",
14 |     "postinstall": "./node_modules/bower/bin/bower install"
15 |   },
16 |   "repository": {
17 |     "type": "git",
18 |     "url": "git://github.com/connorgr/gd3prime.git"
19 |   },
20 |   "author": "",
21 |   "license": "ISC",
22 |   "bugs": {
23 |     "url": "https://github.com/connorgr/gd3prime/issues"
24 |   },
25 |   "homepage": "https://github.com/connorgr/gd3prime"
26 | }
27 | 


--------------------------------------------------------------------------------
/src/cna/cna.js:
--------------------------------------------------------------------------------
 1 | import "cnaChart";
 2 | import "cnaStyle";
 3 | 
 4 | gd3.cna = function(params) {
 5 |   var params = params || {},
 6 |       style  = cnaStyle(params.style || {});
 7 | 
 8 |   // cnaChart functions as a partial application, binding the given variables
 9 |   //   into the returned instance.
10 |   return cnaChart(style);
11 | };


--------------------------------------------------------------------------------
/src/cna/cnaData.js:
--------------------------------------------------------------------------------
  1 | function cnaData(data) {
  2 |   function braph(cdata) {
  3 |     var gene = cdata.gene || "",
  4 |         geneinfo = cdata.neighbors || [],
  5 |         region = cdata.region || {}
  6 |         samplesToTypes = cdata.sampleToTypes || {},
  7 |         seg = cdata.segments;
  8 | 
  9 |     var chrm = region.chr,
 10 |         allmin = 0,
 11 |         allmax = 0,
 12 |         minSegXLoc = region.minSegX,
 13 |         maxSegXLoc = region.maxSegX;
 14 | 
 15 |     // Initialize data structures
 16 |     var geneJSON = geneinfo.map(function(d) {
 17 |       var selected = d.name == gene;
 18 |       return { fixed: selected ? true: false , start: d.start, end: d.end, label: d.name, selected: selected };
 19 |     });
 20 | 
 21 |     var sampleTypes = [],
 22 |         samplelst = [],
 23 |         segJSON   = [];
 24 | 
 25 |     // Flatten the segments data
 26 |     seg.forEach(function(d){
 27 |       samplelst.push( d.sample );
 28 | 
 29 |       var dSegments = d.segments;
 30 |       dSegments.forEach(function(s){
 31 |         // create simulated annotation data if it does not exist.
 32 |         // var vote = {
 33 |         //   type: 'vote',
 34 |         //   score: 100
 35 |         // }
 36 |         // var link = {
 37 |         //   type: 'link',
 38 |         //   href: 'http://www.cs.brown.edu',
 39 |         //   text: 'BrownCS'
 40 |         // }
 41 |         // var testAnnotation = [
 42 |         //   {
 43 |         //     type: 'text',
 44 |         //     title: 'Sample',
 45 |         //     text: d.sample
 46 |         //   },
 47 |         //   {
 48 |         //     type: 'table',
 49 |         //     header: ['Cancer', 'PMIDs', 'Votes'],
 50 |         //     data: [
 51 |         //       ['1', link, vote],
 52 |         //       ['4', link, vote]
 53 |         //     ]
 54 |         //   }
 55 |         // ];
 56 | 
 57 |         segJSON.push({
 58 |           // annotation: testAnnotation,
 59 |           gene: gene,
 60 |           start: s.start,
 61 |           end: s.end,
 62 |           label: s.sample,
 63 |           sample: d.sample,
 64 |           dataset: samplesToTypes[d.sample],
 65 |           ty: s.ty
 66 |         })
 67 | 
 68 |         if (sampleTypes.indexOf(samplesToTypes[d.sample]) === -1){
 69 |           sampleTypes.push( samplesToTypes[s.sample] );
 70 |         }
 71 |       });
 72 |     });
 73 | 
 74 | 
 75 |     // Sort the segments by cancer type and then by length
 76 |     segJSON.sort(function(a, b){
 77 |       if (a.dataset != b.dataset) return d3.ascending(a.dataset, b.dataset);
 78 |       else return d3.ascending(a.end-a.start, b.end-b.start);
 79 |     });
 80 | 
 81 |     var sampleTypeToInclude = {};
 82 |     sampleTypes.sort().forEach(function(d){ sampleTypeToInclude[d] = true; });
 83 | 
 84 |     var d = {
 85 |       genes: geneJSON,
 86 |       sampleTypes: sampleTypes,
 87 |       samplesToTypes: samplesToTypes,
 88 |       segments: segJSON,
 89 |       segmentDomain: [minSegXLoc, maxSegXLoc],
 90 |       sampleTypeToInclude: sampleTypeToInclude
 91 |     };
 92 | 
 93 |     d.get = function(arg) {
 94 |       if (arg == 'genes') return d.genes;
 95 |       else if (arg == 'sampleTypes') return d.sampleTypes;
 96 |       else if (arg == 'samplesToTypes') return d.samplesToTypes;
 97 |       else if (arg == 'segments') return d.segments;
 98 |       else if (arg == 'amps') return d.amps;
 99 |       else if (arg == 'dels') return d.dels;
100 |       else if (arg == 'segmentDomain') return d.segmentDomain;
101 |       else return undefined;
102 |     }
103 | 
104 |     // We stack amplifications above and deletions below the
105 |     // genome bar, so we need to figure out which position in 
106 |     // the stack each *visible* segment has
107 |     d.recomputeSegmentIndices = function(){
108 |       var ampIndex = 0,
109 |           delIndex = 0;
110 | 
111 |       d.segments.forEach(function(datum){
112 |         if (d.sampleTypeToInclude[datum.dataset]){
113 |           if (datum.ty == "amp") datum.index = ampIndex++;
114 |           if (datum.ty == "del") datum.index = delIndex++;
115 |         }
116 |       });
117 |       d.numAmps = ampIndex;
118 |       d.numDels = delIndex;
119 |     }
120 |     d.recomputeSegmentIndices();
121 | 
122 |     return d;
123 |   }
124 |   var cnaData = braph(data);
125 | 
126 |   return cnaData;
127 | }


--------------------------------------------------------------------------------
/src/cna/cnaStyle.js:
--------------------------------------------------------------------------------
 1 | function cnaStyle(style) {
 2 |   return {
 3 |     fontFamily: style.fontFamily || '"HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif',
 4 |     fontSize: style.fontSize || '12px',
 5 |     geneColor: style.geneColor || '#aaa',
 6 |     backgroundColor: style.backgroundColor || '#f6f6f6',
 7 |     geneHeightOverflow: style.geneHeightOverflow || 5,
 8 |     geneHighlightColor: style.geneHighlightColor || '#f00',
 9 |     geneSelectedColor: style.geneSelectedColor || '#f00',
10 |     genomeBarHeight: style.genomeBarHeight || 14,
11 |     height: style.height || 400, // only works if scrolling is activated
12 |     horizontalBarHeight: style.horizontalBarHeight || 5,
13 |     horizontalBarSpacing: style.horizontalBarSpacing || 6,
14 |     width: style.width || 500,
15 |     margin: style.margin || {top: 10, right: 20, bottom: 10, left: 0}
16 |   };
17 | }


--------------------------------------------------------------------------------
/src/cna/index.js:
--------------------------------------------------------------------------------
1 | import "cna.js";


--------------------------------------------------------------------------------
/src/core/class.js:
--------------------------------------------------------------------------------
 1 | // Thanks goes to mbostock and D3 implementation
 2 | // https://github.com/mbostock/d3/blob/master/src/core/class.js
 3 | 
 4 | function gd3_class(ctor, properties) {
 5 |   try {
 6 |     for (var key in properties) {
 7 |       Object.defineProperty(ctor.prototype, key, {
 8 |         value: properties[key],
 9 |         enumerable: false
10 |       });
11 |     }
12 |   } catch (e) {
13 |     ctor.prototype = properties;
14 |   }
15 | }


--------------------------------------------------------------------------------
/src/core/color.js:
--------------------------------------------------------------------------------
  1 | gd3.color = {};
  2 | 
  3 | gd3.color.noData = '#eeeeee';
  4 | 
  5 | gd3.color.categoryPalette;
  6 | gd3.color.annotationPalettes = {};
  7 | gd3.color.annotationToType = {};
  8 | 
  9 | gd3.color.palettes = {};
 10 | 
 11 | // colorbrewer paired qualitative paired scale with modified 2 and 1 element versions
 12 | // Color blind safe!
 13 | gd3.color.palettes.categorical_cbSafe = {
 14 |   1: ["#1f78b4"],
 15 |   2: ["#1f78b4","#b2df8a"],
 16 |   3: ["#a6cee3","#1f78b4","#b2df8a"],
 17 |   4: ["#a6cee3","#1f78b4","#b2df8a","#33a02c"]
 18 | };
 19 | 
 20 | // colorbrewer paired qualitative paired scale, but above range of colorblind friendly
 21 | // Even though the two use the same scale, they are separated for clarity
 22 | gd3.color.palettes.categorical = {
 23 |   5: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99"],
 24 |   6: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c"],
 25 |   7: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f"],
 26 |   8: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00"],
 27 |   9: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6"],
 28 |   10: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6","#6a3d9a"],
 29 |   11: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6","#6a3d9a","#ffff99"],
 30 |   12: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6","#6a3d9a","#ffff99","#b15928"]
 31 | };
 32 | 
 33 | gd3.color.palettes.annotation_discrete = [
 34 |   ["#ad494a", "#a55194", "#8ca252", "#8c6d31",  "#843c39", "#393b79", "#7b4173", "#637939", "#e7ba52", "#bd9e39", "#cedb9c", "#ce6dbd", "#d6616b", "#9c9ede", "#b5cf6b", "#5254a3", "#e7969c", "#6b6ecf", "#e7cb94", "#de9ed6"],
 35 |   ["#fd8d3c", "#31a354", "#9e9ac8", "#969696", "#756bb1", "#3182bd", "#636363", "#e6550d", "#a1d99b", "#74c476", "#fdd0a2", "#bdbdbd", "#bcbddc", "#c6dbef", "#fdae6b", "#6baed6", "#dadaeb", "#9ecae1", "#c7e9c0", "#d9d9d9"]
 36 | ];
 37 | 
 38 | // These default to the colorbrewer sequential, single-hue palettes
 39 | // The blue scale has been discluded because of its use for the heatmap chart
 40 | // Additionally, the ordering of scales is made to be as colorblind-friendly as possible
 41 | gd3.color.palettes.annotation_continuous = [
 42 |   ['rgb(247,252,245)','rgb(0,68,27)'],
 43 |   ['rgb(252,251,253)','rgb(63,0,125)'],
 44 |   ['rgb(240,240,240)','rgb(0,0,0)'],
 45 |   ['rgb(255,245,235)','rgb(127,39,4)'],
 46 |   ['rgb(255,245,240)','rgb(103,0,13)']
 47 | ];
 48 | 
 49 | // The behavior for annotations is as follows:
 50 | // annotations() : return the annotation palette object
 51 | // annotations(key) : return the annotation palette object key's value
 52 | // annotation(key, data) : set the annotation key's palette to have a domain of data
 53 | //   --> The scale will default to discrete, unless data.length == 2 && typeof(each datum) == Number
 54 | // annotation(key, data, type) : as before, except hardcode scale as "discrete" or "continuous"
 55 | // annotation(key, data, type, colors) : as before, except hardcode in palette colors
 56 | gd3.color.annotations = function() {
 57 |   if(arguments.length == 0) return gd3.color.annotationPalettes;
 58 |   if(arguments.length == 1) return gd3.color.annotationPalettes[arguments[0]];
 59 |   // Else, expect two arguments where the first is the name and the second is the type
 60 |   if(Object.prototype.toString.call(arguments[1]) !== '[object Array]' ) {
 61 |     throw 'annotations() must be passed: (1) the annotation name, (2) an array of annotation values'
 62 |         + ' OR the range of values, (3) [optionally] a string declaring if the data is "discrete"'
 63 |         + ' or "continuous"';
 64 |   }
 65 |   if(arguments.length > 2 && arguments[2] != "discrete" && arguments[2] != "continuous") {
 66 |     throw 'annotations() third argument must either be "discrete" or "continuous"';
 67 |   }
 68 | 
 69 |   var scale;
 70 | 
 71 |   var annotation = arguments[0],
 72 |       data = arguments[1];
 73 | 
 74 |   // Assign scale type
 75 |   var type;
 76 |   if(arguments.length > 2) type = arguments[2];
 77 |   else if(data.length == 2 && typeof(data[0]) === 'number' && typeof(data[1]) === 'number') type = 'continuous';
 78 |   else type = 'discrete';
 79 | 
 80 |   gd3.color.annotationToType[annotation] = type;
 81 | 
 82 |   // Define the type of scale and the domain
 83 |   if(type == 'continuous') {
 84 |     scale = d3.scale.linear().domain([d3.min(data),d3.max(data)]);
 85 |   } else {
 86 |     scale = d3.scale.ordinal().domain(data);
 87 |   }
 88 | 
 89 |   // Define the color scale range of the annotation
 90 |   var colors;
 91 |   if(arguments.length > 3) {
 92 |     if(Object.prototype.toString.call(arguments[3]) !== '[object Array]' ) {
 93 |       throw 'annotations()\'s third argument must be an array of colors you wish to use in your annotation scale';
 94 |     }
 95 |     colors = arguments[3];
 96 |   } else {
 97 |     var numOfType = Object.keys(gd3.color.annotationPalettes).filter(function(d) {
 98 |           return gd3.color.annotationToType[d] == type;
 99 |         }).length, // # of previously defined of this type of scale
100 |         palettes = gd3.color.palettes;
101 | 
102 |         var paletteIndex;
103 |         if(type == 'discrete') {
104 |           paletteIndex = (numOfType + 1) % palettes.annotation_discrete.length;
105 |         } else {
106 |           paletteIndex = (numOfType + 1) % palettes.annotation_continuous.length;
107 |         }
108 | 
109 |         var palette = (type == 'discrete' ? palettes.annotation_discrete : palettes.annotation_continuous)[paletteIndex];
110 | 
111 |     colors = palette;
112 |   }
113 |   scale.range(colors);
114 | 
115 |   // Define the annotation scale in the annotationPalettes object
116 |   gd3.color.annotationPalettes[annotation] = scale;
117 | }
118 | 
119 | // Create a palette for category data (e.g., cancer type) given the categories
120 | //  or given categories and colors
121 | // If no arguments are given, the function returns the current palette
122 | gd3.color.categories = function() {
123 |   function isArrayTest() {
124 |     for(var i = 0; i < arguments.length; i++) {
125 |       var a = arguments[i];
126 |       if( Object.prototype.toString.call(a) !== '[object Array]' ) {
127 |         throw 'categories() must be passed: (1) an array of categories, (2) an array of categories'
128 |             + ' and an array of colors';
129 |       }
130 |       if(a.length == 0) throw 'categories() must be passed non-empty arrays for arguments';
131 |     }
132 |   }
133 | 
134 |   if(arguments.length == 0) return gd3.color.categoryPalette;
135 |   else if(arguments.length == 1) {
136 |     var categories = arguments[0];
137 |     isArrayTest(categories);
138 | 
139 |     var colors;
140 |     if(categories.length < 5) {
141 |       colors = gd3.color.palettes.categorical_cbSafe[categories.length];
142 |     } else if (categories.length < 13) {
143 |       colors = gd3.color.palettes.categorical[categories.length];
144 |     } else {
145 |       colors = d3.scale.category20().range();
146 |     }
147 | 
148 |     gd3.color.categoryPalette = d3.scale.ordinal().domain(categories).range(colors);
149 |   } else if(arguments.length > 1) {
150 |     var categories = arguments[0],
151 |         colors = arguments[1];
152 | 
153 |     isArrayTest(categories, colors);
154 |     gd3.color.categoryPalette = d3.scale.ordinal().domain(categories).range(colors);
155 |   }
156 | 
157 |   return gd3.color.categoryPalette;
158 | }


--------------------------------------------------------------------------------
/src/core/dataStructures.js:
--------------------------------------------------------------------------------
 1 | var gd3_data_structures = {
 2 |   UnionFind: function(){
 3 |     // Instance variables
 4 |     var weights = {},
 5 |       parents = {};
 6 | 
 7 |     // Find and return the name of the set containing the object
 8 |     function get(x){
 9 |       // check for previously unknown object
10 |       if (!(x in parents)){
11 |         parents[x] = x;
12 |         weights[x] = 1;
13 |         return x;
14 |       } else {
15 |         // find path of objects leading to the root
16 |         var path = [x],
17 |           root = parents[x],
18 |           count = 0;
19 | 
20 |         while (root != path[path.length - 1] && count <= 15){
21 |           path.push( root );
22 |           root = parents[root];
23 |           count++;
24 |         }
25 | 
26 |         // compress the path and return
27 |         path.forEach(function(ancestor){
28 |           parents[ancestor] = root;
29 |         });
30 | 
31 |         return root;
32 |       }
33 |     }
34 | 
35 |     // Find the sets containing the objects and merge them all
36 |     function union(xs){
37 |       // Convert xs to a list if it isn't one already
38 |       if (xs.constructor != Array){
39 |         xs = [xs];
40 |       }
41 | 
42 |       // Merge all sets containing any x in xs
43 |       var roots = xs.map(get),
44 |         heaviest = d3.max(roots.map(function(r){ return [weights[r], r]; }))[1];
45 | 
46 |       roots.forEach(function(r){
47 |         if (r != heaviest){
48 |           weights[heaviest] += weights[r];
49 |           parents[r] = heaviest;
50 |         }
51 |       });
52 |     }
53 | 
54 |     // Return a list of lists containing each group
55 |     function groups(){
56 |       var groupIndex = 0,
57 |         groupToIndex = {},
58 |         currentGroups = [[]];
59 | 
60 |       Object.keys(parents).forEach(function(n){
61 |         var group = get(n);
62 |         if (!(group in groupToIndex)) groupToIndex[group] = groupIndex++;
63 |         if (currentGroups.length <= groupToIndex[group]) currentGroups.push([]);
64 |         currentGroups[groupToIndex[group]].push( +n );
65 |       });
66 | 
67 |       return currentGroups;
68 |     }
69 | 
70 |     return { get: get, union: union, groups: groups }; 
71 |   }
72 | }
73 | 


--------------------------------------------------------------------------------
/src/core/index.js:
--------------------------------------------------------------------------------
1 | import "class";
2 | import "color";
3 | import "util";
4 | import "dataStructures";


--------------------------------------------------------------------------------
/src/core/util.js:
--------------------------------------------------------------------------------
 1 | var gd3_util = {
 2 |   arraysEqual: function(a, b) {
 3 |         if (a === b) return true;
 4 |         if (a == null || b == null) return false;
 5 |         if (a.length != b.length) return false;
 6 | 
 7 |         // If you don't care about the order of the elements inside
 8 |         // the array, you should sort both arrays here.
 9 | 
10 |         for (var i = 0; i < a.length; ++i) {
11 |           if (a[i] !== b[i]) return false;
12 |         }
13 |         return true;
14 |       },
15 |   arrayToSet: function(a) {
16 |     var seen = {};
17 |     return a.filter(function(item) {
18 |       return seen.hasOwnProperty(item) ? false : (seen[item] = true);
19 |     });
20 |   },
21 |   allPairs: function(xs){
22 |     var n = xs.length,
23 |         pairs = [];
24 | 
25 |     for (var i = 0; i < n; i++){
26 |       for (var j = i+1; j < n; j++){
27 |         pairs.push( [xs[i], xs[j]] );
28 |       }
29 |     }
30 |     return pairs;
31 |   },
32 |   selectionSize: function(selection){
33 |     var n = 0;
34 |     selection.each(function() { ++n; });
35 |     return n;
36 |   }
37 | }


--------------------------------------------------------------------------------
/src/dendrogram/dendrogram.js:
--------------------------------------------------------------------------------
 1 | import "../core/util.js"
 2 | import "../core/dataStructures.js"
 3 | import "dendrogramChart";
 4 | import "dendrogramStyle";
 5 | 
 6 | gd3.dendrogram = function(params) {
 7 |   var params = params || {},
 8 |       style  = dendrogramStyle(params.style || {});
 9 | 
10 |   // dendrogramChart functions as a partial application, binding the given variables
11 |   //   into the returned instance.
12 |   return dendrogramChart(style);
13 | };


--------------------------------------------------------------------------------
/src/dendrogram/dendrogramChart.js:
--------------------------------------------------------------------------------
  1 | import "dendrogramData.js";
  2 | 
  3 | function dendrogramChart(style) {
  4 |   // Globals controllable by the user
  5 |   var update,
  6 |       currentDelta,
  7 |       cutAndUpdate,
  8 |       showSlider = false,
  9 |       useLogScale = false;
 10 | 
 11 |   function chart(selection) {
 12 |     selection.each(function(inputData) {
 13 |       ///////////////////////////////////////////////////////////////////
 14 |       // Perform simple validation of data
 15 |       // Z: N-1 x 4 linkage matrix, where N is the number of leaves. Each
 16 |       //    row stores which two nodes (columns 1 and 2) merge at distance
 17 |       //     (column 3). See Scipy for details: http://goo.gl/nycOCS
 18 |       // labels: array of labels (strings). Labels will be drawn in the order
 19 |       //          given in this array.
 20 |       if (!inputData.Z || !inputData.labels){
 21 |         throw "dendrogram: Z and labels *required*."
 22 |       }
 23 | 
 24 |       // Parse the given data into the data structures we'll be using
 25 |       var T = treeFromLinkageMatrix(inputData);
 26 |       data = dendrogramData(inputData, currentDelta, T);
 27 | 
 28 |       // Make sure that there is a unique index in the 4th column
 29 |       var indices = data.Z.map(function(r){ return r[3]; });
 30 |       if (indices.length != d3.set(indices).values().length){
 31 |         data.Z.forEach(function(r, i){
 32 |           r[3] = i + "-" + r[3];
 33 |         })
 34 |       }
 35 | 
 36 |       ///////////////////////////////////////////////////////////////////
 37 |       // Give some of the style elements shorter variable handles
 38 |       var height = style.height,
 39 |         width = style.width,
 40 |         treeWidth,
 41 |         colorScheme = style.colorScheme, // name of color scheme
 42 |         colorSchemes = style.colorSchemes;
 43 | 
 44 |       // Set up the SVG
 45 |       var svg = d3.select(this).selectAll('svg')
 46 |           .data([data]).enter()
 47 |           .append('svg')
 48 |           .attr("xmlns", "http://www.w3.org/2000/svg"),
 49 |         fig = svg.append("g"),
 50 |         edges = fig.append("g").attr("id" ,"edges"), // add edges first so they are shown below nodes
 51 |         leafGroup = fig.append("g").attr("id", "leaves");
 52 | 
 53 |       svg.attr('id', 'figure')
 54 |         .attr('height', height)
 55 |         .attr('width', width)
 56 |         .style('font-family', style.fontFamily)
 57 |         .style('font-size', style.fontSize);
 58 | 
 59 |       // Set up the x-axis
 60 |       var xAxis = d3.svg.axis(),
 61 |           xAxisGroup = fig.append("g")
 62 |             .style({'stroke': style.fontColor, 'fill': 'none', 'stroke-width': style.strokeWidth})
 63 |             .attr("transform", "translate(0," + height + ")");
 64 | 
 65 |       // Set up colors
 66 |       if (!(colorScheme in colorSchemes)){
 67 |         colorScheme = "default";
 68 |       }
 69 |       var color = colorSchemes[colorScheme];
 70 | 
 71 |       ///////////////////////////////////////////////////////////////////
 72 |       // Update redraws the dendrogram using the given treeData
 73 |       update = function (treeData){
 74 |         // Parse the data into shorter variable handles
 75 |         var Z = treeData.Z,
 76 |             labels = treeData.labels,
 77 |             labelToGroup = treeData.labelToGroup,
 78 |             n = labels.length;    // number of nodes
 79 | 
 80 |         if (!treeData.labelToGroup){
 81 |           labelToGroup = {};
 82 |           labels.forEach(function(d, i){ labelToGroup[d] = i; });
 83 |         }
 84 | 
 85 |         // Create a mapping of leaves (labels) to when they first are
 86 |         // added, and then sort the labels in this order
 87 |         function isLeaf(v){ return v < n; }
 88 |         var nodeToIndex = [];
 89 |         labels.forEach(function(n, i){ nodeToIndex[i] = i; });
 90 | 
 91 |         // Set up a linear y-axis scale
 92 |         var y = d3.scale.linear()
 93 |             .domain([0, labels.length-1])
 94 |             .range([style.nodeRadius, height-style.nodeRadius]),
 95 |           labelToY = d3.scale.ordinal() // convenience scale for labels directly
 96 |             .domain(labels)
 97 |             .rangePoints([style.nodeRadius, height-style.nodeRadius]);
 98 | 
 99 |         ///////////////////////////////////////////////////////////////
100 |         // LEAVES' GENERAL UPDATE
101 | 
102 |         // DATA JOIN: join data with old elements
103 |         var leaves = leafGroup.selectAll("g")
104 |           .data(labels, function(d){ return d; });
105 | 
106 |         // UPDATE: transition old elements
107 |         leaves.transition()
108 |           .duration(style.animationSpeed)
109 |           .attr("transform", function(d){ return "translate(0," + labelToY(d) + ")"; });
110 | 
111 |         leaves.select("circle")
112 |           .attr("fill", function(d){ return color(labelToGroup[d]); });
113 | 
114 |         // ENTER: create new elements
115 |         var leafGs = leaves.enter()
116 |           .append("g")
117 |           .attr("transform", function(d){ return "translate(0," + labelToY(d) + ")"; });
118 | 
119 |         leafGs.append("circle")
120 |           .attr("r", style.nodeRadius)
121 |           .style("fill-opacity", 1e-6)
122 |           .attr("fill", function(d){ return color(labelToGroup[d]); })
123 |           .transition()
124 |           .duration(style.animationSpeed)
125 |           .style("fill-opacity", 1);
126 | 
127 |         leafGs.append("text")
128 |           .attr("text-anchor", "start")
129 |           .attr("x", style.nodeRadius + 5)
130 |           .attr("y", style.nodeRadius/2)
131 |           .text(function(d){ return d; });
132 | 
133 |         // EXIT: remove old elements
134 |         leaves.exit().transition()
135 |           .duration(style.animationSpeed)
136 |           .style("fill-opacity", 1e-6)
137 |           .remove();
138 | 
139 |         ///////////////////////////////////////////////////////////////
140 |         // Set up the linear x-axis scale by:
141 | 
142 |         // (1) Compute the size of the largest label, so we can 
143 |         // set the tree width
144 |         var labelWidth = leafGroup.node().getBBox().width;
145 |         treeWidth = width - labelWidth - style.margins.left;
146 |         leafGroup.attr("transform", "translate(" + treeWidth + ",0)");
147 | 
148 |         // (2) Using the updated treeWidth to set up the x-axis scale
149 |         var dists = Z.map(function(row){ return row[2]; }),
150 |             xExtent = d3.extent(dists);
151 | 
152 |         if (useLogScale) x = d3.scale.log();
153 |         else x = d3.scale.linear()
154 |         x.domain(xExtent)
155 |          .range([treeWidth, style.margins.left]); // go in reverse, since low distances are to the furthest right
156 | 
157 |         ///////////////////////////////////////////////////////////////
158 |         // Create objects to represent each edge
159 |         var edgeData = [],
160 |             distances = labels.map(function(_){ return xExtent[0]; })
161 |             groups = labels.map(function(d){ return [labelToGroup[d]]; });
162 | 
163 |         function connectNodes(u, v, w, index){
164 |           // Find the y-index of each node
165 |           var i  = nodeToIndex[u],
166 |               j  = nodeToIndex[v],
167 |               d1 = distances[u],
168 |               d2 = distances[v],
169 |               g1 = groups[u],
170 |               g2 = groups[v],
171 |               newG = g1.length == 1 && g2.length == 1 && g1[0] == g2[0] ? g1 : g1.concat(g2);
172 | 
173 |           // Draw the horizontal line from u
174 |           edgeData.push({name: "u" + index, x1: x(d1), x2: x(w), y1: y(i), y2: y(i), groups: g1 });
175 | 
176 |           // Draw the horizontal line from v
177 |           edgeData.push({name: "v" + index, x1: x(d2), x2: x(w), y1: y(j), y2: y(j), groups: g2 });
178 | 
179 |           // Connect the two horizontal lines with a vertical line
180 |           edgeData.push({name: "uv" + index, x1: x(w), x2: x(w), y1: y(i), y2: y(j), groups: newG })
181 | 
182 |           // Add an index for the new internal nodes
183 |           nodeToIndex.push( (i  + j) / 2. );
184 |           distances.push(w);
185 |           groups.push( newG );
186 | 
187 |         }
188 | 
189 |         Z.forEach(function(row){ connectNodes(row[0], row[1], row[2], row[3]); });
190 | 
191 |         ///////////////////////////////////////////////////////////////
192 |         // EDGES' GENERAL UPDATE
193 |         // Data join
194 |         var lines = edges.selectAll("line")
195 |           .data(edgeData, function(d){ return d.name + " " + d.ty; });
196 | 
197 |         // Transition existing elements
198 |         lines.transition()
199 |           .duration(style.animationSpeed)
200 |           .attr("x1", function(d){ return d.x1; })
201 |           .attr("x2", function(d){ return d.x2; })
202 |           .attr("y1", function(d){ return d.y1; })
203 |           .attr("y2", function(d){ return d.y2; })
204 |           .attr("stroke-dasharray", function(d){
205 |             if (d.groups.length == 1){ return ""; }
206 |             else { return ("3", "3"); }
207 |           });
208 | 
209 |         // Add new elements
210 |         lines.enter()
211 |           .append("line")
212 |           .attr("x1", function(d){ return d.x1; })
213 |           .attr("x2", function(d){ return d.x1; })
214 |           .attr("y1", function(d){ return d.y1; })
215 |           .attr("y2", function(d){ return d.y1; })
216 |           .attr("stroke", style.strokeColor)
217 |           .attr("stroke-width", style.strokeWidth)
218 |           .attr("stroke-dasharray", function(d){
219 |             if (d.groups.length == 1){ return ""; }
220 |             else { return ("3", "3"); }
221 |           })
222 |           .attr("fill-opacity", 1e-6)
223 |           .transition()
224 |             .duration(style.animationSpeed)
225 |             .attr("x2", function(d){ return d.x2; })
226 |             .attr("y2", function(d){ return d.y2; })
227 |             .attr("fill-opacity", 1);
228 | 
229 |         // Fade and remove old elements
230 |         lines.exit().transition()
231 |           .duration(style.animationSpeed)
232 |           .style("stroke-opacity", 1e-6)
233 |           .remove();
234 | 
235 |         ///////////////////////////////////////////////////////////////////
236 |         // Update the x-axis
237 |         xAxis.scale(x);
238 |         xAxisGroup.call(xAxis);
239 |         xAxisGroup.selectAll("text")
240 |           .style({'stroke-width': '0px', 'fill': style.fontColor });
241 | 
242 |         ///////////////////////////////////////////////////////////////////
243 |         // Resize the SVG to make sure everything fits
244 |         svg.attr('height', fig.node().getBBox().height);
245 |       }
246 | 
247 |       // Draw the inital dendrogram
248 |       update(data);
249 | 
250 |       // Show the slider if necessary
251 |       if (showSlider){
252 |         // Create the data
253 |         var U = gd3_data_structures.UnionFind(),
254 |             N = inputData.labels.length,
255 |             step = Math.ceil(N/100), // only sample points after every N/100 merges
256 |             series = [{values: [], name: "Largest component"},
257 |                       {values: [], name: "Non-singleton components"}];
258 |         
259 |         inputData.Z.forEach(function(row, i){
260 |           // Merge nodes row[0] and row[1] with their parent
261 |           U.union([row[0], row[1], N+i]);
262 | 
263 |           // Record the largest and number of non-singleton components
264 |           // every N/100 merges
265 |           if (i % step == 0){
266 |             var groups = U.groups(),
267 |                 largestSize = d3.max(groups, function(g){ return g.length; }),
268 |                 nonSingletons = d3.sum(groups.map(function(g){ return g.length > 1; }));
269 |               if (row[2] != 0){
270 |                 series[0].values.push({x: row[2], y: largestSize });
271 |                 series[1].values.push({x: row[2], y: nonSingletons });
272 |               }
273 |           }
274 |         });
275 | 
276 |         var allPoints = d3.merge(series.map(function(d, i){ return d.values; }));
277 | 
278 |         // Set up the sizes
279 |         var sliderWidth = treeWidth - style.sliderMargins.left - style.sliderMargins.right,
280 |             sliderHeight = style.sliderHeight - style.sliderMargins.top - style.sliderMargins.bottom;
281 | 
282 |         // Set up the scales
283 |         if (useLogScale) sliderX = d3.scale.log().range([0, sliderWidth]);
284 |         else sliderX = d3.scale.linear().range([0, sliderWidth]);
285 | 
286 |         var yExtent = d3.extent(allPoints, function(d){ return d.y; });
287 |         if (yExtent[1] - yExtent[0] > 100) sliderY = d3.scale.log().range([sliderHeight, 0]);
288 |         else sliderY = d3.scale.linear().range([sliderHeight, 0]);
289 | 
290 |         sliderX.domain( d3.extent(allPoints, function(d) { return d.x; }).reverse() );
291 |         sliderY.domain( yExtent ).nice();
292 | 
293 |         // Set up the axes
294 |         var sliderColor = d3.scale.category10(),
295 |             sliderXAxis = d3.svg.axis()
296 |               .scale(sliderX)
297 |               .orient("bottom"),
298 |             sliderYAxis = d3.svg.axis()
299 |               .scale(sliderY)
300 |               .ticks(5)
301 |               .orient("left"),
302 |             line = d3.svg.line()
303 |               .interpolate("basis")
304 |               .x(function(d) { return sliderX(d.x); })
305 |               .y(function(d) { return sliderY(d.y); });
306 | 
307 |         // Add the instructions and the SVG
308 |         d3.select(this).insert("div", "svg")
309 |           .html("<b>Instructions</b>: Choose &delta; by mousing over the plot below and double-clicking. You can change your selection by double-clicking again.<br/><br/>")
310 | 
311 |         var sliderSVG = d3.select(this).insert("svg", "svg")
312 |           .attr("width", sliderWidth + style.sliderMargins.left + style.sliderMargins.right)
313 |           .attr("height", sliderHeight + style.sliderMargins.top + style.sliderMargins.bottom)
314 |           .append("g")
315 |           .attr("transform", "translate(" + style.sliderMargins.left + "," + style.sliderMargins.top + ")")
316 |           .style("font-size", style.fontSize);
317 | 
318 |         sliderSVG.append("rect") // background
319 |           .attr("width", sliderWidth + style.sliderMargins.left + style.sliderMargins.right)
320 |           .attr("height", sliderHeight + style.sliderMargins.top + style.sliderMargins.bottom)
321 |           .attr("fill", style.backgroundColor);
322 | 
323 |         // Draw the lines
324 |         var lines = sliderSVG.selectAll(".point")
325 |           .data(series)
326 |           .enter().append("g")
327 |           .attr("class", "point");
328 | 
329 |         lines.append("path")
330 |           .attr("class", "line")
331 |           .attr("d", function(d) { return line(d.values); })
332 |           .style("fill", "none")
333 |           .style("stroke", function(d) { return sliderColor(d.name); });
334 | 
335 |         // Add the axes
336 |         sliderSVG.append("g")
337 |           .attr("class", "x axis")
338 |           .attr("transform", "translate(0," + sliderHeight + ")")
339 |           .call(sliderXAxis)
340 |             .append("text")
341 |             .attr("x", sliderWidth/2)
342 |             .attr("dy", "30px")
343 |             .style("text-anchor", "middle")
344 |             .text("\u03B4");
345 | 
346 |         sliderSVG.append("g")
347 |           .attr("class", "y axis")
348 |           .call(sliderYAxis);
349 | 
350 |         sliderSVG.selectAll(".axis path")
351 |           .style({fill: "none", stroke: "#000", "shape-rendering": "crispEdges"});
352 |         sliderSVG.selectAll(".axis line")
353 |           .style({fill: "none", stroke: "#000", "shape-rendering": "crispEdges"});
354 | 
355 |         // Add a series legend, aligned to the right topmost corner of the plot
356 |         var legend = sliderSVG.append("g"),
357 |             legendGroups = legend.selectAll(".legend-text")
358 |               .data(series).enter()
359 |               .append("g");
360 | 
361 |         legendGroups.append("line")
362 |           .attr("x1", 0)
363 |           .attr("x1", 20)
364 |           .attr("y1", 0)
365 |           .attr("y2", 0)
366 |           .style("stroke", function(d) { return sliderColor(d.name); });
367 | 
368 |         legendGroups.append("text").attr("x", 25).attr("y", 3).text(function(d){ return d.name; });
369 | 
370 |         var legendWidth = legend.node().getBBox().width;
371 |         legendGroups.attr("transform", function(d, i){
372 |           var thisX = treeWidth - legendWidth - style.sliderMargins.left,
373 |               thisY = sliderY(d3.max(sliderY.domain())) + (i)*15;
374 |           return "translate(" + thisX + "," + thisY + ")";
375 |         });
376 | 
377 |         // Add the onmouseover line that we use to select delta
378 |         var deltaFixed = false,
379 |             deltaFormat = d3.format(".5r"),
380 |             deltaLine = sliderSVG.append("line")
381 |               .attr("y1", sliderY(d3.min(sliderY.domain())))
382 |               .attr("y2", sliderY(d3.max(sliderY.domain())))
383 |               .style("fill", "none")
384 |               .style("stroke", style.strokeColor)
385 |               .style("opacity", 0),
386 |             delta = sliderSVG.append("text")
387 |               .attr("text-anchor", "start")
388 |               .attr("x", treeWidth - legendWidth - style.sliderMargins.left)
389 |               .attr("y", sliderY(d3.max(sliderY.domain())) + (series.length*15) + 5)
390 |               .text("\u03B4: " + deltaFormat(d3.max(sliderX.domain())));
391 | 
392 |         // Move the line to match the mouse position
393 |         sliderSVG.on("mousemove", function(){
394 |           var coordinates = d3.mouse(this);
395 |           if (!deltaFixed && coordinates[0] > 0){
396 |             deltaLine.attr("x1", coordinates[0])
397 |               .attr("x2", coordinates[0])
398 |               .style("opacity", 1);
399 |           }
400 |         });
401 | 
402 |         // On double click update the plot with the given delta
403 |         sliderSVG.on("dblclick", function(){
404 |           // Fix the delta on double click if it wasn't before
405 |           if (!deltaFixed){
406 |             currentDelta = sliderX.invert(deltaLine.attr("x1"));
407 |             cutAndUpdate();
408 |           }
409 |           deltaFixed = !deltaFixed;
410 |         });
411 | 
412 |       }
413 | 
414 |       // Cut the plot using the current value of delta, 
415 |       // then update the dendrogram accordingly
416 |       cutAndUpdate = function(){
417 |         // Update the value shown in the delta plot
418 |         if (showSlider) delta.text("\u03B4: " + deltaFormat(currentDelta));
419 |         update(cutDendrogram(inputData, currentDelta, T));
420 |       }
421 |     });
422 |   }
423 | 
424 |   // "Public" functions that the user can call
425 |   chart.update = function(treeData){
426 |     update(treeData);
427 |     return chart;
428 |   }
429 | 
430 |   chart.animationSpeed = function(){
431 |     return style.animationSpeed; // note this returns the animation speed, NOT the chart
432 |   }
433 | 
434 |   chart.showSlider = function(){
435 |     showSlider = true;
436 |     return chart;
437 |   }
438 | 
439 |   chart.setDelta = function(delta){
440 |     currentDelta = delta;
441 |     if (cutAndUpdate) cutAndUpdate(delta);
442 |     return chart;
443 |   };
444 | 
445 |   chart.logScale = function(_){
446 |     if (arguments.length) useLogScale = _; 
447 |     return chart;
448 |   };
449 | 
450 |   return chart;
451 | }


--------------------------------------------------------------------------------
/src/dendrogram/dendrogramData.js:
--------------------------------------------------------------------------------
  1 | function dendrogramData(inputData, delta, T) {
  2 |   // Set delta to merge everything (unless it was set already)
  3 |   if (!delta) delta = inputData.Z[inputData.Z.length-1][2];
  4 | 
  5 |   // Cut the dendrogram accordingly and return
  6 |   return cutDendrogram(inputData, delta, T);
  7 | }
  8 | 
  9 | function cutDendrogram(data, delta, T){
 10 |   function MRCA(u, v){
 11 |     var parentsU = [],
 12 |         parentsV = [],
 13 |         node = u;
 14 | 
 15 |     while (node != null){
 16 |       node = T[node].parent;
 17 |       parentsU.push(node);
 18 |     }
 19 | 
 20 |     node = v;
 21 |     while (node != null){
 22 |       node = T[node].parent;
 23 |       if (parentsU.indexOf(node) != -1){
 24 |         return T[node].weight;
 25 |       }
 26 |     }
 27 |     return 0;
 28 |   }
 29 | 
 30 |   function subtreeDistance(t1, t2){ return MRCA(d3.max(t1), d3.max(t2)); }
 31 |   function isLeaf(v){ return v < N; }
 32 | 
 33 |   // Declarations
 34 |   var Z = [], labelToGroup = {}, groupLabels = {}, groupIndex = 0,
 35 |       rows = data.Z.filter(function(row){ return row[2] <= +delta; })
 36 |                    .map(function(row, i){ return row.slice(0, 3).concat([i]); }),
 37 |       n = rows.length,
 38 |       N = data.labels.length;
 39 | 
 40 |   // Add all the nodes that are below the cut value to the UnionFind
 41 |   var U = gd3_data_structures.UnionFind(),
 42 |       leafIndices = [];
 43 | 
 44 |   rows.forEach(function(row, i){
 45 |     U.union([row[0], row[1], N+i]);
 46 |     if (isLeaf(row[0])) leafIndices.push(row[0]);
 47 |     if (isLeaf(row[1])) leafIndices.push(row[1]);
 48 |   });
 49 | 
 50 |   leafIndices = leafIndices.sort(function(i, j){ return d3.ascending(+i, +j); });
 51 |   var labels = leafIndices.map(function(i){ return data.labels[i]; });
 52 | 
 53 |   // Then extract the labels that will still be required, normalizing
 54 |   // the rows to match their new numbers
 55 |   function addIfLeaf(v){
 56 |     // Ignore internal nodes, leaving the row unchanged
 57 |     if (!isLeaf(v)) return v;
 58 | 
 59 |     // Record leaves and assign them to groups
 60 |     var group = U.get(v);
 61 |     if (!(group in groupLabels)) groupLabels[group] = groupIndex++;
 62 |     // labels.push(data.labels[v]);
 63 |     labelToGroup[data.labels[v]] = groupLabels[group];
 64 | 
 65 |     // Relabel the leaf to its new index
 66 |     return leafIndices.indexOf(v);
 67 |   }
 68 | 
 69 |   rows.forEach(function(row, i){
 70 |     row[0] = addIfLeaf(row[0]);
 71 |     row[1] = addIfLeaf(row[1]);
 72 |   });
 73 | 
 74 |   // Normalize the values of each internal node (we can only
 75 |   // do this once we know the number of labels)
 76 |   var m = labels.length;
 77 |   rows.forEach(function(row){
 78 |     if (row[0] >= m) row[0] -= N - m;
 79 |     if (row[1] >= m) row[1] -= N - m;
 80 |   });
 81 | 
 82 |   // Compute the pseudoedges
 83 |   var groups = U.groups().map(function(g){
 84 |         return {members: g, _id: d3.max(g) - N + m};
 85 |       }),
 86 |       pairs = gd3_util.allPairs(groups),
 87 |       d = {};
 88 | 
 89 |   pairs.forEach(function(P){
 90 |     var dist = subtreeDistance(P[0].members, P[1].members);
 91 |     if (!d[P[0]._id]) d[P[0]._id] = {};
 92 |     if (!d[P[1]._id]) d[P[1]._id] = {};
 93 |     d[P[0]._id][P[1]._id] = dist;
 94 |     d[P[1]._id][P[0]._id] = dist;
 95 |   });
 96 | 
 97 |   var iterations = 0;
 98 |   while (pairs.length > 0){
 99 |     // Some sanity checking so the browser won't crash even if this infinitely loops
100 |     if (iterations > 10000) throw new Error("This while loop shouldn't execute 10k times.")
101 |     iterations++;
102 | 
103 |     // Identify the pair with minimum distance
104 |     var toMerge, lowest = Number.MAX_VALUE;
105 |     pairs.forEach(function(P, i){
106 |       if (d[P[0]._id][P[1]._id] < lowest){
107 |         lowest = d[P[0]._id][P[1]._id]
108 |         toMerge = P;
109 |       }
110 |     });
111 | 
112 |     // Add that link to the linkage matrix
113 |     rows.push([toMerge[0]._id, toMerge[1]._id, lowest, rows.length]);
114 | 
115 |     // Remove the groups/pairs that include either of the merged pairs
116 |     var idsToRemove = [toMerge[0]._id, toMerge[1]._id];
117 |     groups = groups.filter(function(G){ return idsToRemove.indexOf(G._id) === -1; });
118 |     pairs = pairs.filter(function(P){
119 |       return idsToRemove.indexOf(P[0]._id) === -1 &&
120 |            idsToRemove.indexOf(P[1]._id) === -1;
121 |     });
122 | 
123 |     // Add new pairs including the new group
124 |     var newGroup = { _id: m + rows.length-1,
125 |              members: d3.merge([toMerge[0].members, toMerge[1].members])
126 |             };
127 |     d[newGroup._id] = {};
128 | 
129 |     groups.forEach(function(G){
130 |       var dist = d3.min([d[toMerge[0]._id][G._id], d[toMerge[1]._id][G._id]]);
131 |       pairs.push([G, newGroup]);
132 |       d[G._id][newGroup._id] = dist;
133 |       d[newGroup._id][G._id] = dist;
134 |     });
135 |     groups.push(newGroup);
136 |   }
137 | 
138 |   Z = rows.map(function(row){ return row.slice(0); });
139 | 
140 |   return { Z: Z, labels: labels, labelToGroup: labelToGroup };
141 | }
142 | 
143 | ///////////////////////////////////////////////////////////////////////////
144 | // Create a tree to represent the linkage matrix and make it easy to
145 | // compute distances between subtrees
146 | function treeFromLinkageMatrix(data){
147 |   var N = data.labels.length,
148 |       T = {};
149 | 
150 |   data.Z.forEach(function(row, i){
151 |     T[N+i] = { children: [row[0], row[1]], weight: row[2], parent: null };
152 |     if (!(row[0] in T)) T[row[0]] = {};
153 |     T[row[0]].parent = N+i;
154 |     if (!(row[1] in T)) T[row[1]] = {};
155 |     T[row[1]].parent = N+i;
156 |   });
157 | 
158 |   return T;
159 | }
160 | 


--------------------------------------------------------------------------------
/src/dendrogram/dendrogramStyle.js:
--------------------------------------------------------------------------------
 1 | function dendrogramStyle(style) {
 2 |   return {
 3 |         colorSchemes: style.colorSchemes || {"default": d3.scale.category20() },
 4 |         edgeWidth: style.edgeWidth || 1.5,
 5 |         fontColor: style.fontColor || '#333',
 6 |         backgroundColor: "#fff",
 7 |         fontFamily: style.fontFamily || '"HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif',
 8 |         fontSize: style.fontSize || 12,
 9 |         margins: style.margins || {bottom: 0, left: 5, right: 0, top: 0},
10 |         nodeRadius: style.nodeRadius || 10,
11 |         width: style.width || 1200,
12 |         height: style.height || 600,
13 |         strokeWidth: style.strokeWidth || 1,
14 |         strokeColor: style.strokeColor || "#333",
15 |         colorScheme: style.colorScheme || "default",
16 |         animationSpeed: style.animationSpeed || 750,
17 |         margins: { left: 40, right: 0, top: 0, bottom: 0},
18 |         sliderMargins: { left: 40, right: 0, top: 5, bottom: 20},
19 |         sliderHeight: 125
20 |     }
21 | }


--------------------------------------------------------------------------------
/src/dendrogram/index.js:
--------------------------------------------------------------------------------
1 | import "dendrogram.js"


--------------------------------------------------------------------------------
/src/dispatch/dispatch.js:
--------------------------------------------------------------------------------
1 | gd3.dispatch = d3.dispatch('sample', 'interaction', 'sort', 'filterCategory', 'filterType', 'mutation', 'filterMutationType');
2 | 
3 | // filter dataset is akin to filtering by cancer type, since each cancer type is its own dataset
4 | // filter cell type is akin to filtering by insertion or deletion mutations, since they are a datatype within a dataset
5 | 


--------------------------------------------------------------------------------
/src/dispatch/index.js:
--------------------------------------------------------------------------------
1 | import "dispatch";


--------------------------------------------------------------------------------
/src/end.js:
--------------------------------------------------------------------------------
1 |   if (typeof define === 'function' && define.amd) define(gd3);
2 |   else if (typeof module === 'object' && module.exports) module.exports = gd3;
3 |   this.gd3 = gd3;
4 | }();


--------------------------------------------------------------------------------
/src/gd3.js:
--------------------------------------------------------------------------------
 1 | import "start.js";
 2 | import "dispatch/";
 3 | import "core/";
 4 | import "cna/";
 5 | import "dendrogram/";
 6 | import "graph/";
 7 | import "heatmap/";
 8 | import "mutmtx/";
 9 | import "scatterplot/";
10 | import "tooltip/";
11 | import "transcript/";
12 | import "end.js";


--------------------------------------------------------------------------------
/src/graph/graph.js:
--------------------------------------------------------------------------------
 1 | import "graphChart.js";
 2 | import "graphStyle.js";
 3 | 
 4 | gd3.graph = function(params) {
 5 |   var params = params || {},
 6 |       style  = graphStyle(params.style || {});
 7 | 
 8 |   // graphChart functions as a partial application, binding the given variables
 9 |   //   into the returned instance.
10 |   return graphChart(style);
11 | };


--------------------------------------------------------------------------------
/src/graph/graphChart.js:
--------------------------------------------------------------------------------
  1 | import "graphData.js";
  2 | 
  3 | function graphChart(style) {
  4 |   var anchorNodesOnClick = true,
  5 |       drawLegend = true;
  6 | 
  7 |   function chart(selection) {
  8 |     selection.each(function(data) {
  9 |       data = graphData(data);
 10 | 
 11 |       // Used for edge classes and filtering
 12 |       var instanceIDConst = 'gd3-graph-'+Date.now();
 13 | 
 14 |       var height = style.height,
 15 |           width = style.width;
 16 | 
 17 |       var svg = d3.select(this)
 18 |           .selectAll('svg')
 19 |           .data([data])
 20 |           .enter()
 21 |             .append('svg')
 22 |                 .attr('height', height)
 23 |                 .attr('width', width)
 24 |                 .style('font-family', style.fontFamily)
 25 |                 .style('font-size', style.fontSize);
 26 | 
 27 |       var graph = svg.append('g');
 28 | 
 29 |       // Set up edge coloring
 30 |       var edgeColor = d3.scale.ordinal()
 31 |           .domain(data.edgeCategories)
 32 |           .range(style.edgeColors);
 33 | 
 34 |       // Set up node coloring
 35 |       var nodeColor = d3.scale.linear()
 36 |           .domain([data.minNodeValue, data.maxNodeValue])
 37 |           .range(style.nodeColor)
 38 |           .interpolate(d3.interpolateLab);
 39 | 
 40 |       var forceHeight = height,
 41 |           forceWidth = width;
 42 | 
 43 |       if(drawLegend) {
 44 |         var legend = svg.append('g');
 45 |         drawLegendFn(legend);
 46 |       }
 47 | 
 48 |       // Set up force directed graph
 49 |       var force = d3.layout.force()
 50 |           .charge(-400)
 51 |           .linkDistance(100)
 52 |           .size([forceWidth,forceHeight]);
 53 | 
 54 |       var x = d3.scale.linear().range([0,forceWidth]),
 55 |           y = d3.scale.linear().range([0,forceHeight]);
 56 | 
 57 |       // Start the force directed layout
 58 |       force.nodes(data.nodes).links(data.links).start();
 59 | 
 60 |       // Draw the edges
 61 |       var link = graph.append('g').selectAll('.link')
 62 |           .data(data.links)
 63 |           .enter()
 64 |           .append('g')
 65 |           .attr('class', 'gd3Link');
 66 | 
 67 |       // Draw categories for each edge
 68 |       if(data.edgeCategories) {
 69 |         link.each(function(d) {
 70 |           var thisEdge = d3.select(this);
 71 |           d.categories.forEach(function(c) {
 72 |             thisEdge.append('line')
 73 |                 .attr('class', instanceIDConst+'-'+c)
 74 |                 .style('stroke-width', style.edgeWidth)
 75 |                 .style('stroke', edgeColor(c));
 76 |           });
 77 |         });
 78 |       } else {
 79 |         link.append('line').style('stroke-width', style.edgeWidth).style('stroke', edgeColor(null));
 80 |       }
 81 | 
 82 |       link.selectAll('line').style('stroke-linecap', 'round');
 83 | 
 84 | 
 85 |       // Draw the nodes
 86 |       var node = graph.append('g').selectAll('.node')
 87 |           .data(data.nodes)
 88 |           .enter()
 89 |           .append('g')
 90 |               .style('cursor', 'move')
 91 |               .attr('class', 'gd3Node')
 92 |               .call(force.drag);
 93 | 
 94 |       node.append('circle')
 95 |           .attr('r', style.nodeRadius)
 96 |           .attr('fill', function(d) { return nodeColor(d.value); })
 97 |           .style('stroke-width', style.nodeStrokeWidth)
 98 |           .style('stroke', style.nodeStrokeColor);
 99 | 
100 |       node.append('text')
101 |           .attr('x', style.nodeRadius+style.nodeLabelPadding)
102 |           .attr('y', style.nodeRadius+style.nodeLabelPadding)
103 |           .style('font-family', style.fontFamily)
104 |           .style('font-size', style.fontSize)
105 |           .style('font-weight', style.nodeLabelFontWeight)
106 |           .text(function(d) { return d.name; });
107 | 
108 |       force.on('tick', function() {
109 |         node.attr('transform', function(d) {
110 |           var maxBound = style.nodeRadius+style.nodeStrokeWidth,
111 |               minBoundX = forceWidth - style.nodeRadius - style.nodeStrokeWidth,
112 |               minBoundY = forceHeight - style.nodeRadius - style.nodeStrokeWidth;
113 |           if(drawLegend) maxBoundX = maxBound + style.legendWidth;
114 |           else maxBoundX = maxBound;
115 |           d.x = Math.max(maxBoundX, Math.min(minBoundX, d.x));
116 |           d.y = Math.max(maxBound, Math.min(minBoundY, d.y));
117 |           return 'translate('+ d.x + ',' + d.y + ')';
118 |         });
119 | 
120 |         // position the edges
121 |         link.each(function(d) {
122 |           var thisEdgeSet = d3.select(this),
123 |               categories = d.categories || [null],
124 |               numCategories = categories.length;
125 | 
126 |           var offset = (numCategories/2) * style.edgeWidth;
127 | 
128 |           thisEdgeSet.selectAll('line').each(function(d,i) {
129 |             var thisEdge = d3.select(this);
130 |             thisEdge.attr('x1', d.source.x - offset + style.edgeWidth * i)
131 |                 .attr('x2', d.target.x - offset + style.edgeWidth * i)
132 |                 .attr('y1', d.source.y - offset + style.edgeWidth * i)
133 |                 .attr('y2', d.target.y - offset + style.edgeWidth * i);
134 |           });
135 |         });
136 |       });
137 | 
138 |       if(anchorNodesOnClick) {
139 |         force.drag().on('dragstart', function(d) {
140 |           d.fixed = true;
141 |           //d3.select(this).select('circle').style('stroke-opacity', 0);
142 |         });
143 |         node.on('dblclick', function(d) {
144 |           d.fixed = d.fixed ? false : true;
145 |           //d3.select(this).select('circle').style('stroke-opacity', 1);
146 |         });
147 |       } // end anchorNodesOnClick block
148 | 
149 | 
150 |       function drawLegendFn(legend) {
151 |         legend.style('font-family', style.fontFamily);
152 |         legend.append('rect')
153 |             .attr('width',style.legendWidth)
154 |             .attr('height', style.height)
155 |             .style('fill', '#ffffff')
156 |             .style('opacity', .95);
157 | 
158 |         var title = legend.append('text')
159 |             .style('font-size', style.legendFontSize);
160 | 
161 |         title.selectAll('tspan')
162 |             .data(data.title.split('\n'))
163 |             .enter()
164 |             .append('tspan')
165 |                 .attr('x', 0)
166 |                 .attr('dy', style.legendFontSize+2)
167 |                 .text(function(d){ return d; });
168 | 
169 |         // Render the scale
170 |         var titleHeight = title.node().getBBox().height + 4,
171 |             scaleG = legend.append('g')
172 |                 .attr('transform','translate(0,'+titleHeight+')');
173 |         scaleG.append('text')
174 |             .attr('x', style.legendScaleWidth + 2)
175 |             .attr('y', style.legendFontSize)
176 |             .style('font-size', style.legendFontSize)
177 |             .text(data.maxNodeValue);
178 |         scaleG.append('text')
179 |                 .attr('x', style.legendScaleWidth + 2)
180 |                 .attr('y', style.height/2)
181 |                 .style('font-size', style.legendFontSize)
182 |                 .text(data.minNodeValue);
183 |         var colorScaleRect = scaleG.append('rect')
184 |             .attr('height', style.height/2)
185 |             .attr('width', style.legendScaleWidth)
186 |             .attr('class', 'gd3GraphGradientLegend');
187 | 
188 |         // Create a unique ID for the color map gradient in case multiple graphs are made
189 |         var now = Date.now(),
190 |             gradientId = 'gd3-graph-gradient'+now;
191 | 
192 |         // Configure the gradient to be mapped on to the legend
193 |         var gradient = scaleG.append('svg:defs')
194 |               .append('svg:linearGradient')
195 |                 .attr('id', gradientId)
196 |                 .attr('x1', '0%')
197 |                 .attr('y1', '100%')
198 |                 .attr('x2', '0%')
199 |                 .attr('y2', '0%');
200 | 
201 |         var scaleRange = nodeColor.range();
202 |         scaleRange.forEach(function(c, i){
203 |           gradient.append('svg:stop')
204 |               .attr('offset', i*1./(scaleRange.length-1))
205 |               .attr('stop-color', c)
206 |               .attr('stop-opacity', 1);
207 |         });
208 | 
209 |         colorScaleRect.attr('fill', 'url(#'+gradientId+')');
210 | 
211 |         // Add the edge keys to the graph
212 |         var scaleHeight = scaleG.node().getBBox().height + 4,
213 |             edgeKeys = legend.append('g').attr('class', 'gd3GraphNetworkLegend').selectAll('g')
214 |                 .data(data.edgeCategories)
215 |                 .enter()
216 |                 .append('g')
217 |                     .style('cursor', 'pointer')
218 |                     .on('click', function(category) {
219 |                       var catEdges = d3.selectAll('.'+instanceIDConst+'-'+category),
220 |                           visible = catEdges.style('opacity') == 1;
221 |                       d3.select(this).style("opacity", visible ? 0.5 : 1);
222 |                       catEdges.style('opacity', visible ? 0 : 1);
223 |                     })
224 |                     .on('mouseover', function() {
225 |                       d3.select(this).selectAll('text').style('fill', 'red');
226 |                     })
227 |                     .on('mouseout', function() {
228 |                       d3.select(this).selectAll('text').style('fill', 'black');
229 |                     });
230 |         edgeKeys.each(function(category, i) {
231 |           var thisEl = d3.select(this),
232 |               thisY = (i+1)*style.legendFontSize + titleHeight + scaleHeight;
233 |           thisEl.append('line')
234 |               .attr('x1', 0)
235 |               .attr('y1', thisY - style.legendFontSize/4)
236 |               .attr('x2', 15)
237 |               .attr('y2', thisY - style.legendFontSize/4)
238 |               .style('stroke', edgeColor(category))
239 |               .style('stroke-width', style.legendFontSize/2);
240 | 
241 |           thisEl.append('text')
242 |               .attr('x', 16)
243 |               .attr('y', (i+1)*style.legendFontSize + titleHeight + scaleHeight)
244 |               .style('font-size', style.legendFontSize)
245 |               .text(category);
246 |         });
247 |       }
248 | 
249 |       // Add dispatch
250 |       link.on("click.dispatch-interaction", function(d){
251 |         gd3.dispatch.interaction({ source: d.source.name, target: d.target.name });
252 |       })
253 |     });
254 |   }
255 | 
256 |   chart.clickAnchorsNodes = function(state) {
257 |     anchorNodesOnClick = state;
258 |     return chart;
259 |   }
260 | 
261 |   chart.showLegend = function(state) {
262 |     drawLegend = state;
263 |     return chart;
264 |   }
265 | 
266 |   return chart;
267 | }
268 | 


--------------------------------------------------------------------------------
/src/graph/graphData.js:
--------------------------------------------------------------------------------
 1 | function graphData(inputData) {
 2 |   var data = {
 3 |     edges : [],
 4 |     nodes : []
 5 |   }
 6 | 
 7 | 
 8 |   function defaultParse () {
 9 |     data.title = inputData.title || '';
10 |     data.edges = inputData.edges;
11 |     data.nodes = inputData.nodes;
12 |     data.links = loadLinks(data.edges,data.nodes);
13 | 
14 |     data.maxNodeValue = d3.max(data.nodes.map(function(d) { return d.value; }));
15 |     data.minNodeValue = d3.min(data.nodes.map(function(d) { return d.value; }));
16 | 
17 |     data.edgeCategories = [];
18 | 
19 |     // add edge categories only if they exist
20 |     var categories = {};
21 |     if(data.edges.length && data.edges[0].categories) {
22 |       data.edges.forEach(function(e) {
23 |         e.categories.forEach(function(c) {
24 |           categories[c] = null;
25 |         });
26 |       });
27 |       data.edgeCategories = Object.keys(categories);
28 |     }
29 | 
30 |     // creates a force-directed layout friendly link list
31 |     function loadLinks(edges, nodes) {
32 |       var links = [],
33 |           nodeToIndex = {};
34 | 
35 |       nodes.forEach(function(n, i){ nodeToIndex[n.name] = i; });
36 |       edges.forEach(function(d){
37 |         links.push({
38 |           source: nodes[nodeToIndex[d.source]],
39 |           target: nodes[nodeToIndex[d.target]],
40 |           weight: d.weight,
41 |           categories: d.categories,
42 |           references: d.references
43 |         });
44 |       });
45 | 
46 |       return links;
47 |     } // end loadLinks()
48 |   }
49 | 
50 |   defaultParse();
51 | 
52 |   return data;
53 | }


--------------------------------------------------------------------------------
/src/graph/graphStyle.js:
--------------------------------------------------------------------------------
 1 | function graphStyle(style) {
 2 |   return {
 3 |     edgeColors : style.edgeColors || d3.scale.category10().range(),
 4 |     edgeWidth : style.edgeWidth || 3,
 5 |     fontFamily : style.fontFamily || '"HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif',
 6 |     fontSize : style.fontSize || 12,
 7 |     height : style.height || 200,
 8 |     legendFontSize : style.legendFontSize || 11,
 9 |     legendScaleWidth : style.legendScaleWidth || 30,
10 |     legendWidth : style.legendWidth || 75,
11 |     margins : style.margins || {bottom: 0, left: 0, right: 0, top: 0},
12 |     nodeColor : style.nodeColor || ['#ccc','#ccc'],
13 |     nodeRadius : style.nodeRadius || 10,
14 |     nodeLabelPadding : style.nodeLabelPadding || 2,
15 |     nodeLabelFontWeight : style.nodeLabelFontWeight || 'bold',
16 |     nodeStrokeColor : style.nodeStrokeColor || '#333',
17 |     nodeStrokeWidth : style.nodeStrokeWidth || 2,
18 |     width : style.width || 300,
19 |   };
20 | }


--------------------------------------------------------------------------------
/src/graph/index.js:
--------------------------------------------------------------------------------
1 | import "graph.js";


--------------------------------------------------------------------------------
/src/heatmap/heatmap.js:
--------------------------------------------------------------------------------
 1 | import "heatmapChart.js";
 2 | import "heatmapStyle.js";
 3 | 
 4 | gd3.heatmap = function(params) {
 5 |   var params = params || {},
 6 |       style  = heatmapStyle(params.style || {});
 7 | 
 8 |   // heatmapChart functions as a partial application, binding the given variables
 9 |   //   into the returned instance.
10 |   return heatmapChart(style);
11 | };


--------------------------------------------------------------------------------
/src/heatmap/heatmapData.js:
--------------------------------------------------------------------------------
 1 | function heatmapData(inputData) {
 2 |   var data = {
 3 |     annotations : undefined,
 4 |     cells : [],
 5 |     maxCellValue : Number.NEGATIVE_INFINITY,
 6 |     minCellValue : Number.POSITIVE_INFINITY,
 7 |     xs : [],
 8 |     ys : []
 9 |   }
10 | 
11 | 
12 |   function defaultParse () {
13 |     data.cells = inputData.cells;
14 |     data.name = inputData.name;
15 |     data.xs = inputData.xs;
16 |     data.ys = inputData.ys;
17 | 
18 |     data.annotations = inputData.annotations;
19 | 
20 |     // Find max and min values to make color scale
21 |     var tmp;
22 |     for (var i=data.cells.length-1; i>=0; i--) {
23 |       tmp = data.cells[i].value;
24 |       if (tmp > data.maxCellValue) data.maxCellValue = tmp;
25 |       if (tmp < data.minCellValue) data.minCellValue = tmp;
26 |     }
27 | 
28 |     var datasetCatIndex = -1;
29 |     if(data.annotations) {
30 |       if(!data.annotations.annotationToColor) data.annotations.annotationToColor = {};
31 | 
32 |       data.annotations.categories.forEach(function(category, categoryIndex) {
33 |         var entry = data.annotations.annotationToColor[category];
34 |         if(entry && Object.keys(entry).length > 0) return;
35 | 
36 |         // Assume the data is continuous and find the min and max of the category
37 |         var annotationNames = Object.keys(data.annotations.sampleToAnnotations),
38 |             values = annotationNames.map(function(n) {
39 |               return data.annotations.sampleToAnnotations[n][categoryIndex];
40 |             });
41 | 
42 |         entry = [d3.min(values), d3.max(values)];
43 | 
44 |         data.annotations.annotationToColor[category] = entry;
45 | 
46 |       });
47 |       // Set any missing column datasets to null
48 |       data.annotations.categories.forEach(function(c, i){
49 |         if (c.toLowerCase() === "cancer type" || c.toLowerCase() === "dataset"){
50 |           datasetCatIndex = i;
51 |         }
52 |       })
53 |     }
54 | 
55 |     // If this category is giving the dataset (or cancer type) of the
56 |     // column, add it to the map of column IDs to datasets
57 |     data.columnIdToDataset = {};
58 |     if (datasetCatIndex !== -1){
59 |       data.xs.forEach(function(n){
60 |         data.columnIdToDataset[n] = data.annotations.sampleToAnnotations[n][datasetCatIndex];
61 |       })
62 |     } else {
63 |       data.xs.forEach(function(n){ data.columnIdToDataset[n] = null; });
64 |     }
65 |   }
66 | 
67 |   defaultParse();
68 | 
69 |   data.sortColumns = function (columnIds) {
70 |     data.xs.sort(function(a,b) { return columnIds.indexOf(a) - columnIds.indexOf(b); });
71 |   }
72 | 
73 | 
74 |   return data;
75 | }
76 | 


--------------------------------------------------------------------------------
/src/heatmap/heatmapStyle.js:
--------------------------------------------------------------------------------
 1 | function heatmapStyle(style) {
 2 |   return {
 3 |     annotationCellHeight : style.annotationCellHeight || 10,
 4 |     annotationCategorySpacing : style.annotationCategorySpacing || 5,
 5 |     annotationContinuousColorScale : style.annotationContinuousColorScale || ['#004529', '#f7fcb9'],
 6 |     annotationLabelFontSize : style.annotationLabelFontSize || style.fontSize || 12,
 7 |     cellHeight : style.cellHeight || 18,
 8 |     cellWidth : style.cellWidth || 14,
 9 |     colorScale : style.colorScale || ['rgb(222,235,247)','rgb(198,219,239)','rgb(158,202,225)','rgb(107,174,214)','rgb(66,146,198)','rgb(33,113,181)','rgb(8,81,156)','rgb(8,48,107)'],
10 |     colorScaleHeight : style.colorScaleHeight || 14,
11 |     colorScaleWidth : style.colorScaleWidth || 200,
12 |     fontFamily : style.fontFamily || '"HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif',
13 |     fontSize : style.fontSize || 14,
14 |     labelMargins : style.labelMargins || {bottom: 5, right: 2},
15 |     margins : style.margins || {bottom: 0, left: 0, right: 0, top: 0},
16 |     noCellValueColor : style.noCellValueColor || '#a7a7a7',
17 |     width : style.width || 400,
18 |   };
19 | }


--------------------------------------------------------------------------------
/src/heatmap/index.js:
--------------------------------------------------------------------------------
1 | import "heatmap.js";


--------------------------------------------------------------------------------
/src/mutmtx/index.js:
--------------------------------------------------------------------------------
1 | import "mutmtx";


--------------------------------------------------------------------------------
/src/mutmtx/mutmtx.js:
--------------------------------------------------------------------------------
 1 | import "../core/class";
 2 | import "mutmtxChart";
 3 | import "mutmtxStyle";
 4 | 
 5 | gd3.mutationMatrix = function(params) {
 6 |   var params = params || {},
 7 |       style  = mutmtxStyle(params.style || {});
 8 | 
 9 |   // mutmtxChart functions as a partial application, binding the given variables
10 |   //   into the returned instance.
11 |   return mutmtxChart(style);
12 | };


--------------------------------------------------------------------------------
/src/mutmtx/mutmtxData.js:
--------------------------------------------------------------------------------
  1 | function mutmtxData(inputData) {
  2 |   var data = {
  3 |     datasets: [],
  4 |     glyphs: ['square', 'triangle-up', 'cross', 'circle', 'diamond', 'triangle-down'],
  5 |     hiddenColumns: {
  6 |       byCategory: [],
  7 |       byType: []
  8 |     },
  9 |     ids: {
 10 |       columns: [],
 11 |       rows: []
 12 |     },
 13 |     labels: {
 14 |       columns: [],
 15 |       rows: []
 16 |     },
 17 |     maps: {
 18 |       cellTypeToTick: inputData.cellTypeToTick || {snv: 'full', amp: 'up', del: 'down'},
 19 |       cellTypeToLabel: inputData.cellTypeToLabel || {snv: 'SNV', inactive_snv: 'Inactivating SNV', amp: 'Amplification', del: 'Deletion'},
 20 |       cellTypeToGlyph: inputData.cellTypeToGlyph || {snv: null, inactive_snv: 'square'},
 21 |       cellTypeToSortIndex: inputData.cellTypeToSortIndex || {snv: 0, inactive_snv: 1, del: 2, amp: 3},
 22 |       columnIdToLabel: {},
 23 |       columnIdToCategory: {},
 24 |       columnIdToTypes: {},
 25 |       rowIdToLabel: {}
 26 |     },
 27 |     matrix: {
 28 |       cells : {},
 29 |       columnIdToActiveRows : {},
 30 |       rowIdToActiveColumns : {}
 31 |     },
 32 |     types: []
 33 |   };
 34 | 
 35 |   data.coverage = function(){
 36 |     var mutatedSamples = d3.merge(data.ids.rows.map(function(d){
 37 |           return data.matrix.rowIdToActiveColumns[d];
 38 |         })),
 39 |         numMutatedSamples = d3.set(mutatedSamples).values().length,
 40 |         s = ((numMutatedSamples*100. / data.numSamples).toFixed(2)) + "%";
 41 |     return s + " (" + numMutatedSamples + "/" + data.numSamples + ")";
 42 |   }
 43 | 
 44 |   data.get = function(attr) {
 45 |     if (!attr) return null;
 46 |     else if (attr === 'datasets') return data.datasets;
 47 |     else if (attr === 'ids') return data.ids;
 48 |     else if (attr === 'labels') return data.labels;
 49 |   }
 50 | 
 51 |   data.reorderColumns = function(ordering) {
 52 |     // Sort by whether or not the column is visible (i.e., has been filtered)
 53 |     function sortByVisibility(c1, c2) {
 54 |       var c1Hidden = data.hiddenColumns.byCategory[c1] || data.hiddenColumns.byType[c1] ? true : false,
 55 |           c2Hidden = data.hiddenColumns.byCategory[c2] || data.hiddenColumns.byType[c2] ? true : false;
 56 | 
 57 |       if (c1Hidden == c2Hidden) return 0;
 58 |       else if (c1Hidden) return 1;
 59 |       else if (c2Hidden) return -1;
 60 |       else return 0;
 61 |     }
 62 | 
 63 |     // Sort by the column's most common cell type
 64 |     function sortByCellType(c1,c2) {
 65 |       var c1Type = data.maps.columnIdToTypes[c1][0],
 66 |           c2Type = data.maps.columnIdToTypes[c2][0];
 67 |       return d3.ascending(data.maps.cellTypeToSortIndex[c1Type], data.maps.cellTypeToSortIndex[c2Type]);
 68 |     }
 69 |     // Sort by how exclusive each column's mutations are with one another
 70 |     function sortByExclusivity(c1, c2) {
 71 |       var c1X = data.matrix.columnIdToActiveRows[c1].length > 1,
 72 |           c2X = data.matrix.columnIdToActiveRows[c2].length > 1;
 73 |       return d3.ascending(c1X, c2X);
 74 |     }
 75 |     // Sort by which column has more "top" activations in the rendered graphic
 76 |     function sortByFirstActiveRow(c1, c2) {
 77 |       var c1First = data.matrix.columnIdToActiveRows[c1][0],
 78 |           c2First = data.matrix.columnIdToActiveRows[c2][0];
 79 |       if (typeof(c1First) == 'undefined') c1First = Number.MAX_VALUE;
 80 |       if (typeof(c2First) == 'undefined') c2First = Number.MAX_VALUE;
 81 |       return d3.ascending(c1First, c2First);
 82 |     }
 83 |     // Sort by the name of the column
 84 |     function sortByName(c1,c2) {
 85 |       var c1Label = data.maps.columnIdToLabel[c1],
 86 |           c2Label = data.maps.columnIdToLabel[c2];
 87 | 
 88 |       return d3.ascending(c1Label, c2Label);
 89 |       //return d3.ascending(data.labels.columns[c1],data.labels.columns[c2]);
 90 |     }
 91 |     // Sort by the column category (i.e, color)
 92 |     function sortByColumnCategory(c1,c2) {
 93 |       return d3.ascending(data.maps.columnIdToCategory[c1], data.maps.columnIdToCategory[c2]);
 94 |     }
 95 | 
 96 |     // Sort the data based on input, or if none, on default ordering
 97 |     var sortFns;
 98 |     if(ordering) {
 99 |       sortFns = [sortByVisibility];
100 |       ordering.forEach(function(d) {
101 |         if(d == 'First active row') sortFns.push(sortByFirstActiveRow);
102 |         if(d == 'Column category') sortFns.push(sortByColumnCategory);
103 |         if(d == 'Exclusivity') sortFns.push(sortByExclusivity);
104 |         if(d == 'Name') sortFns.push(sortByName);
105 |       });
106 |     }
107 |     else {
108 |       sortFns = [sortByVisibility, sortByFirstActiveRow, sortByColumnCategory, sortByExclusivity, sortByCellType, sortByName];
109 |     }
110 | 
111 |     data.ids.columns.sort(function(c1,c2) {
112 |       var sortResult;
113 |       for(var i = 0; i < sortFns.length; i++) {
114 |         sortResult = sortFns[i](c1,c2);
115 |         if (sortResult != 0) {
116 |           return sortResult;
117 |         }
118 |       }
119 |       return sortResult;
120 |     });
121 |   } // end data.reorderColumns()
122 | 
123 |   data.recomputeLabels = function(){
124 |     data.labels.rows = data.labels.rows.map(function(rowLabel){
125 |       var rowId = rowLabel.split(" (")[0],
126 |           count = Object.keys(inputData.M[rowId]).reduce(function(sum, colId){
127 |             if (data.hiddenColumns.byCategory[colId] || data.hiddenColumns.byType[colId]) return sum;
128 |             else return sum + 1;
129 |           }, 0);
130 |       return rowId + " (" + count + ")";
131 |     });
132 |   }
133 | 
134 |   function defaultParse() {
135 |     // Scrape labels from the matrix
136 |     inputData.samples.forEach(function(s) {
137 |       data.maps.columnIdToLabel[s._id] = s.name;
138 |       data.labels.columns.push(s.name);
139 |     });
140 | 
141 |     // Determine the total number of samples across all types
142 |     if (inputData.typeToSamples && inputData.sampleTypes){
143 |       data.numSamples = inputData.sampleTypes.reduce(function(total, t){
144 |         return total + inputData.typeToSamples[t].length;
145 |       },0);
146 |     } else {
147 |       data.numSamples = inputData.samples.length;
148 |     }
149 | 
150 | 	var rowAndCount = [];
151 | 	if (inputData.ordered_row_labels){
152 | 		inputData.ordered_row_labels.forEach(function(k){
153 | 			rowAndCount.push([k,Object.keys(inputData.M[k]).length]);
154 | 		})
155 | 	} else {
156 | 	    Object.keys(inputData.M).forEach(function(k, i) {
157 | 	      // data.maps.rowIdToLabel[i.toString()] = k;
158 | 	      var numSamples = Object.keys(inputData.M[k]).length;
159 | 	      // data.labels.rows.push(k + ' ('+numSamples+')');
160 | 	      rowAndCount.push([k,numSamples]);
161 | 	    });
162 | 
163 | 	    rowAndCount.sort(function(a,b) { return a[1] < b[1] ? 1 : -1; });
164 | 	}
165 | 	var sortedRowIds = [];
166 |     rowAndCount.forEach(function(d, i) {
167 |       var name = d[0],
168 |           numSamples = d[1];
169 |       data.maps.rowIdToLabel[i.toString()] = name;
170 |       data.labels.rows.push(name + ' ('+numSamples+')');
171 |       sortedRowIds.push(name);
172 |     });
173 | 
174 | 
175 |     data.ids.columns = Object.keys(data.maps.columnIdToLabel);
176 |     data.ids.rows = Object.keys(data.maps.rowIdToLabel);
177 | 
178 |     // Make set of datasets in data
179 |     var setOfDatasets = {};
180 |     Object.keys(inputData.sampleToTypes).forEach(function(colId) {
181 |       setOfDatasets[inputData.sampleToTypes[colId]] = null;
182 |       data.maps.columnIdToCategory[colId] = inputData.sampleToTypes[colId];
183 |     });
184 |     data.datasets = Object.keys(setOfDatasets);
185 | 
186 |     // Build matrix data and maps
187 |     var cellTypes = [];
188 |     inputData.samples.forEach(function(d){
189 |       data.matrix.columnIdToActiveRows[d._id] = [];
190 |       data.maps.columnIdToTypes[d._id] = [];
191 |     });
192 | 
193 |     sortedRowIds.forEach(function(rowLabel, rowId) {
194 |       var columns = Object.keys(inputData.M[rowLabel]);
195 |       rowId = rowId.toString();
196 |       // Add rowId -> columns mapping
197 |       data.matrix.rowIdToActiveColumns[rowId] = columns;
198 |       // Add columnId -> row mapping
199 |       columns.forEach(function(colId) {
200 |         // Add the row to the column
201 |         data.matrix.columnIdToActiveRows[colId].push(rowId);
202 | 
203 |         // Add cell data
204 |         var type = inputData.M[rowLabel][colId][0];
205 |         data.matrix.cells[[rowId,colId].join()] = {
206 |           dataset: inputData.sampleToTypes[colId],
207 |           type: inputData.M[rowLabel][colId][0]
208 |         };
209 |         cellTypes.push(type);
210 | 
211 |         // Track the types of cells in the data
212 |         data.maps.columnIdToTypes[colId].push(type);
213 |       });
214 |     }); // end matrix mapping
215 | 
216 |     // Remove repeat types
217 |     data.types = cellTypes.filter(function(item, pos, self) {
218 |       return self.indexOf(item) == pos;
219 |     });
220 | 
221 |     // Process the column to type map s.t. there are no repeats and
222 |     //   the map is ordered by population of each type
223 |     Object.keys(data.maps.columnIdToTypes).forEach(function(colId) {
224 |       var types = data.maps.columnIdToTypes[colId],
225 |           typeLog = {};
226 |       types.forEach(function(t) {
227 |         if(!typeLog[t]) typeLog[t] = 0;
228 |         typeLog[t] = typeLog[t] + 1;
229 |       });
230 | 
231 |       types = Object.keys(typeLog);
232 |       types.sort(function(a,b) { return typeLog[a] < typeLog[b]; });
233 |       data.maps.columnIdToTypes[colId] = types;
234 |     });
235 |     data.types.forEach(function(t){
236 |       if (!(t in data.maps.cellTypeToTick)){
237 |         data.maps.cellTypeToTick[t] = 'full';
238 |       }
239 |       if (!(t in data.maps.cellTypeToLabel)){
240 |         data.maps.cellTypeToLabel[t] = t.replace("_", " ");
241 |       }
242 |     })
243 | 
244 |     // Load the cell type to glyph mapping if it exists, else create it
245 |     if (inputData.cellTypesToGlyph) {
246 |       data.maps.cellTypeToGlyph = inputData.cellTypeToGlyph;
247 |     } else {
248 |       // Remove duplicates from the cellTypes array
249 |       var typesTmp = {};
250 |       cellTypes.forEach(function(t) {
251 |         if(typesTmp[t] == undefined) typesTmp[t] = 0;
252 |         typesTmp[t] = typesTmp[t] + 1;
253 |       });
254 |       var types = Object.keys(typesTmp).sort(function(a,b) { typesTmp[a] > typesTmp[b] });
255 | 
256 |       types.forEach(function(d,i) {
257 |         if (d in data.maps.cellTypeToGlyph) return;
258 |         if (data.maps.cellTypeToTick[d] != 'full'){
259 |           data.maps.cellTypeToGlyph[d] = null;
260 |         } else {
261 |           data.maps.cellTypeToGlyph[d] = data.glyphs[i%data.glyphs.length];
262 |         }
263 |       });
264 |     } // end glyph mapping
265 |   }
266 | 
267 |   defaultParse();
268 | 
269 |   // sample annotation data processing, if present
270 |   if(inputData.annotations) {
271 |     data.annotations = inputData.annotations;
272 |   } else {
273 |     data.annotations = { categories: [], sampleToAnnotations: {}, annotationToColor: {} };
274 |     data.ids.columns.forEach(function(s){
275 |       data.annotations.sampleToAnnotations[data.maps.columnIdToLabel[s]] = [];
276 |     });
277 |   }
278 | 
279 |   // create simulated annotation data if it does not exist.
280 |   // Object.keys(data.matrix.cells).forEach(function(key) {
281 |   //   if (data.matrix.cells[key].annotation == undefined) {
282 |   //     var vote = {
283 |   //       type: 'vote',
284 |   //       score: 100
285 |   //     }
286 |   //     var link = {
287 |   //       type: 'link',
288 |   //       href: 'http://www.cs.brown.edu',
289 |   //       text: 'BrownCS'
290 |   //     }
291 |   //     data.matrix.cells[key].annotation = [
292 |   //       {
293 |   //         type: 'text',
294 |   //         title: 'Sample',
295 |   //         text: key
296 |   //       },
297 |   //       {
298 |   //         type: 'table',
299 |   //         header: ['Cancer', 'PMIDs', 'Votes'],
300 |   //         data: [
301 |   //           ['1', link, vote],
302 |   //           ['4', link, vote]
303 |   //         ]
304 |   //       }
305 |   //     ];
306 |   //   }
307 |   // }); // end simulated annotation data
308 | 
309 |   return data;
310 | }
311 | 


--------------------------------------------------------------------------------
/src/mutmtx/mutmtxStyle.js:
--------------------------------------------------------------------------------
 1 | function mutmtxStyle(style) {
 2 |   return {
 3 |       animationSpeed : style.animationSpeed || 300,
 4 |       annotationContinuousScale : style.annotationContinuousScale || ['#fcc5c0','#49006a'],
 5 |       annotationFontSize : style.annotationFontSize || 10,
 6 |       annotationRowHeight : style.annotationRowHeight || 10,
 7 |       annotationRowSpacing : style.annotationRowSpacing || 5,
 8 |       bgColor : style.bgColor || '#F6F6F6',
 9 |       blockColorMedium : style.blockColorMedium || '#95A5A6',
10 |       blockColorStrongest : style.blockColorStrongest || '#2C3E50',
11 |       boxMargin : style.boxMargin || 5, // assumes uniform margins on all sides
12 |       colorSampleTypes : style.colorSampleTypes || true,
13 |       coocurringColor : style.coocurringColor || 'orange',
14 |       exclusiveColor : style.exclusiveColor || 'blue',
15 |       fontColor : style.fontColor || '#000',
16 |       fontFamily : '"HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif',
17 |       fontSize : style.fontSize || 14,
18 |       glyphColor : style.glyphColor || '#888',
19 |       glyphStrokeColor : style.glyphStrokeColor || '#ccc',
20 |       height : style.height || 300,
21 |       rowHeight : style.rowHeight || 20,
22 |       labelHeight : style.labelHeight || 40,
23 |       labelWidth : style.labelWidth || 100,
24 |       minBoxWidth : style.minBoxWidth || 20,
25 |       mutationLegendHeight : style.mutationLegendHeight || 30,
26 |       sampleStroke : style.sampleStroke || 1,
27 |       sortingMenuFontSize : style.sortingMenuFontSize || 12,
28 |       width : style.width || 600,
29 |       zBottom: 0,
30 |       zTop: 100
31 |   };
32 | }
33 | 


--------------------------------------------------------------------------------
/src/scatterplot/index.js:
--------------------------------------------------------------------------------
1 | import "scatterplot"


--------------------------------------------------------------------------------
/src/scatterplot/scatterplot.js:
--------------------------------------------------------------------------------
1 | import "scatterplotChart.js";
2 | import "scatterplotStyle.js";
3 | 
4 | gd3.scatterplot = function(params) {
5 |   var params = params || {},
6 |       style = scatterplotStyle(params.style || {});
7 | 
8 |   return scatterplotChart(style);
9 | }


--------------------------------------------------------------------------------
/src/scatterplot/scatterplotChart.js:
--------------------------------------------------------------------------------
  1 | import "scatterplotData.js";
  2 | 
  3 | function scatterplotChart(style) {
  4 |   function chart(selection) {
  5 |     selection.each(function(data) {
  6 |       data = scatterplotData(data);
  7 | 
  8 |       // convenience function for rendering the scatterplot points
  9 |       function makeShape(d) {
 10 |         var category = d.category,
 11 |             hasCategory = data.categories.has(category),
 12 |             shape = hasCategory ? style.categoryShapes[data.categories.values().indexOf(category)] : 'circle',
 13 |             pt = d3.svg.symbol().type(shape);
 14 | 
 15 |         return pt.size(style.pointSize * style.pointSize)();
 16 |       }
 17 | 
 18 | 
 19 |       var height = style.height - style.margins.top - style.margins.bottom,
 20 |           width = style.width - style.margins.left - style.margins.right;
 21 | 
 22 |       var pointColor = d3.scale.ordinal().domain(data.categories).range(style.categoryColors);
 23 | 
 24 |       var svg = d3.select(this)
 25 |           .selectAll('svg')
 26 |           .data([data])
 27 |           .enter()
 28 |             .append('svg')
 29 |                 .attr('height', style.height)
 30 |                 .attr('width', style.width)
 31 |                 .attr('xmlns', 'http://www.w3.org/2000/svg')
 32 |                 .style('font-family', style.fontFamily)
 33 |                 .style('font-size', style.fontSize);
 34 | 
 35 |       var scatterplot = svg.append('g').attr('transform', 'translate('+style.margins.left+','+style.margins.top+')');
 36 | 
 37 |       // Construct x and y scales
 38 |       var x = d3.scale.linear().domain([data.xScale.min, data.xScale.max]).range([0, width]),
 39 |           y = d3.scale.linear().domain([data.yScale.min, data.yScale.max]).range([height, 0]);
 40 | 
 41 |       // Construct x and y axis
 42 |       var xAxis = d3.svg.axis().scale(x).orient('bottom'),
 43 |           yAxis = d3.svg.axis().scale(y).orient('left');
 44 | 
 45 |       // Render both axis
 46 |       var axisStyle = { stroke: 'black', fill: 'none','shape-rendering': 'crispEdges', 'stroke-width': '1px'},
 47 |           axisG = scatterplot.append('g').attr('class', 'gd3-scatterplot-axis'),
 48 |           xAxisRender = axisG.append('g')
 49 |               .attr('class', 'x axis')
 50 |               .attr('transform', 'translate(0,' + height + ')')
 51 |               .call(xAxis),
 52 |           xAxisLabel = axisG.append('text')
 53 |               .attr('text-anchor', 'middle')
 54 |               .attr('x', x(x.domain()[1])/2)
 55 |               .attr('y', height + xAxisRender.node().getBBox().height + style.axisFontSize)
 56 |               .style('font-size', style.axisFontSize)
 57 |               .text(data.xLabel),
 58 |           yAxisRender = axisG.append('g')
 59 |               .attr('class', 'y axis')
 60 |               .call(yAxis),
 61 |           yAxisLabel = axisG.append('text')
 62 |               .attr('text-anchor', 'middle')
 63 |               .attr('transform', 'rotate(-90)')
 64 |               .attr('x', -y(y.domain()[0])/2)
 65 |               .attr('y', -yAxisRender.node().getBBox().width)
 66 |               .text(data.yLabel);
 67 | 
 68 |       axisG.selectAll('.tick text').style('fill', 'black').style('font-size', style.axisFontSize);
 69 |       axisG.selectAll('path').style(axisStyle);
 70 | 
 71 |       // Make the title
 72 |       scatterplot.append('text')
 73 |           .attr('text-anchor', 'middle')
 74 |           .attr('x', x(x.domain()[1])/2)
 75 |           .style('font-size', style.titleFontSize)
 76 |           .style('font-weight', 'bold')
 77 |           .text(data.title);
 78 | 
 79 |       // Make the category legend
 80 |       var legendW = style.margins.right - style.legendPadding.left - style.legendPadding.right,
 81 |           legend = scatterplot.append('g')
 82 |               .attr('class', 'gd3-scatterplot-legend')
 83 |               .attr('transform', 'translate('+(width + style.legendPadding.left)+',0)'),
 84 |           legendCategories = legend.selectAll('.category')
 85 |               .data(data.categories.values())
 86 |               .enter()
 87 |               .append('g')
 88 |                   .attr('class', 'category');
 89 | 
 90 |       legendCategories.each(function(d,i) {
 91 |         var thisEl = d3.select(this),
 92 |             shapeR = style.pointSize/2,
 93 |             shape = thisEl.append('path')
 94 |                 .attr('d', makeShape)
 95 |                 .attr('transform', 'translate(' + shapeR + ',' + (-shapeR) + ')')
 96 |                 .style('fill', function(d) { return pointColor(d); }),
 97 |             text = thisEl.append('text')
 98 |                 .attr('x', style.pointSize + 1)
 99 |                 .text(d);
100 | 
101 |         thisEl.attr('transform','translate(0,' + i*(style.legendFontSize+2) + ')');
102 |       });
103 | 
104 |       var pointsGroup = scatterplot.append('g').attr('class', 'gd3-scatterplot-points');
105 |       pointsGroup.selectAll('.point')
106 |           .data(data.pts)
107 |           .enter()
108 |           .append('path')
109 |               .attr('class', 'point')
110 |               .attr('d', makeShape)
111 |               .attr('transform', function(d) { return 'translate(' + x(d.x) + ',' + y(d.y) + ')'; })
112 |               .style('fill', function(d) { return pointColor(d.category); });
113 | 
114 |     });
115 |   }
116 | 
117 | 
118 |   return chart;
119 | }


--------------------------------------------------------------------------------
/src/scatterplot/scatterplotData.js:
--------------------------------------------------------------------------------
 1 | function scatterplotData(inputData) {
 2 |   var data = {
 3 |     categories: [],
 4 |     pts: [],
 5 |     title: '',
 6 |     xLabel: '',
 7 |     xScale: { max: Number.NEGATIVE_INFINITY, min: Number.POSITIVE_INFINITY },
 8 |     yLabel: '',
 9 |     yScale: { max: Number.NEGATIVE_INFINITY, min: Number.POSITIVE_INFINITY }
10 |   }
11 | 
12 |   // categories = Array of Strings
13 |   // pts = Array of Objects s.t. each Object is {x: Number, y: Number},
14 |   //          optionally {x: Number, y: Number, category: String}
15 |   // title = String
16 |   function parseJSON() {
17 |     data.categories = d3.set(inputData.categories ? inputData.categories : []);
18 |     data.pts = inputData.pts.map(function(d) {
19 |       d.x = +(d.x); // safety sanitation
20 |       d.y = +(d.y);
21 | 
22 |       if(d.category) data.categories.add(d.category);
23 | 
24 |       // include range tests to save a loop
25 |       if (!inputData.xScale) {
26 |         data.xScale.max = d3.max([d.x, data.xScale.max]);
27 |         data.xScale.min = d3.min([d.x, data.xScale.min]);
28 |       }
29 |       if (!inputData.yScale) {
30 |         data.yScale.max = d3.max([d.y, data.yScale.max]);
31 |         data.yScale.min = d3.min([d.y, data.yScale.min]);
32 |       }
33 | 
34 |       return d;
35 |     });
36 | 
37 |     data.title = inputData.title;
38 | 
39 |     data.xLabel = inputData.xLabel;
40 |     data.yLabel = inputData.yLabel;
41 | 
42 |     if (inputData.xScale) data.xScale = inputData.xScale;
43 |     if (inputData.yScale) data.yScale = inputData.yScale;
44 |   }
45 | 
46 |   parseJSON();
47 | 
48 |   return data;
49 | }


--------------------------------------------------------------------------------
/src/scatterplot/scatterplotStyle.js:
--------------------------------------------------------------------------------
 1 | function scatterplotStyle(style) {
 2 |   return {
 3 |     axisFontSize : style.axisFontSize || style.fontSize || 12,
 4 |     categoryColors : d3.scale.category10().range(),
 5 |     categoryShapes : ['circle', 'diamond', 'cross', 'triangle-down', 'square', 'triangle-up'],
 6 |     fontFamily : style.fontFamily || '"HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif',
 7 |     fontSize : style.fontSize || 12,
 8 |     height : style.height || 300,
 9 |     legendFontSize : style.legendFontSize || 11,
10 |     legendScaleWidth : style.legendScaleWidth || 30,
11 |     legendWidth : style.legendWidth || 75,
12 |     pointSize : style.pointSize || 7,
13 |     titleFontSize : style.titleFontSize || 14,
14 |     width : style.width || 300,
15 | 
16 |     // Margins defines the chart rendering space whereas the margins serve as gutters for things
17 |     //  like the x axis ticks and labels and the chart title to be positioned
18 |     margins : style.margins || {bottom: 50, left: 35, right: 15, top: style.titleFontSize || 14},
19 |     legendPadding : { top: 0, right: 0, bottom: 0, left: style.pointSize || 7 }
20 |   };
21 | }


--------------------------------------------------------------------------------
/src/start.js:
--------------------------------------------------------------------------------
1 | !function() {
2 |   var gd3 = {version: '0.2.1'};


--------------------------------------------------------------------------------
/src/tooltip/annotationView-old.js:
--------------------------------------------------------------------------------
  1 | function annotationView(style, votingFns) {
  2 |   // Global variables for the annotation
  3 |   var point = null,
  4 |       svg = null,
  5 |       target = null;
  6 | 
  7 |   var votingFns = votingFns || {};
  8 | 
  9 |   function view(selection) {
 10 |     // Append text to the annotation view
 11 |     function appendText(selection, data) {
 12 |       var title = data.title ? data.title+': ' : '',
 13 |           text = data.text ? data.text : '';
 14 |       selection.append('p')
 15 |         .style('color', '#fff')
 16 |         .style('font-family', style.fontFamily)
 17 |         .style('font-size', style.fontSize)
 18 |         .style('margin', '0px')
 19 |         .style('padding', '0px')
 20 |         .text(title+text);
 21 |     }
 22 | 
 23 |     // Append link to the annotation view
 24 |     function appendLink(selection, data) {
 25 |       selection.append('a')
 26 |         .attr('href', data.href)
 27 |         .style('color', '#fff')
 28 |         .style('font-family', style.fontFamily)
 29 |         .style('font-size', style.fontSize)
 30 |         .style('margin', '0px')
 31 |         .style('padding', '0px')
 32 |         .text(data.text);
 33 |     }
 34 | 
 35 |     // Append a table to the annotation view
 36 |     function appendTable(selection, data) {
 37 |       var table = selection.append('table'),
 38 |           header = table.append('thead').append('tr'),
 39 |           body = table.append('tbody');
 40 | 
 41 |       table.style({
 42 |         'border-collapse': 'collapse',
 43 |         'border-bottom': '2px solid #ccc',
 44 |         'border-top': '2px solid #ccc',
 45 |         'margin-top': '3px'
 46 |       });
 47 |       header.style('border-bottom', '1px solid #ccc');
 48 |       header.selectAll('td')
 49 |           .data(data.header)
 50 |           .enter()
 51 |           .append('td')
 52 |               .style('color', '#fff')
 53 |               .style('font-family', style.fontFamily)
 54 |               .style('font-size', style.fontSize)
 55 |               .style('margin', '0px')
 56 |               .style('padding', '0 5px 2px 0')
 57 |               .text(function(d) { return d; });
 58 | 
 59 |       var rows = body.selectAll('tr')
 60 |           .data(data.data)
 61 |           .enter()
 62 |           .append('tr');
 63 | 
 64 |       var cells = rows.selectAll('td')
 65 |           .data(function(d) { return d; })
 66 |           .enter()
 67 |           .append('td')
 68 |               .style('max-width', '115px')
 69 |               .style('padding', '0 3px 0 3px')
 70 |               .each(function(d) {
 71 |                 if(typeof(d) === 'string') {
 72 |                   appendText(d3.select(this), {text:d});
 73 |                 } else if (d.type === 'vote') {
 74 |                   appendVote(d3.select(this), d);
 75 |                 } else if (d.type === 'link') {
 76 |                   appendLink(d3.select(this), d);
 77 |                 }
 78 |           });
 79 |     }
 80 | 
 81 |     // Append a voting counter
 82 |     function appendVote(selection, data) {
 83 |       var down = null,
 84 |           score = null,
 85 |           up = null;
 86 | 
 87 |       var defaultColor = 'rgb(255, 255, 255)',
 88 |           activeColor = 'rgb(255, 165, 0)';
 89 | 
 90 |       function abstractVote(clickedArrow, otherArrow) {
 91 |         var upvote = clickedArrow == up,
 92 |             adjust = upvote ? 1 : -1;
 93 | 
 94 |         var scoreDatum = score.datum();
 95 | 
 96 |         if (clickedArrow.style('color') == defaultColor) {
 97 |           // fix vote if the other vote direction active
 98 |           if (otherArrow.style('color') == activeColor) {
 99 |             score.text( parseInt(score.text()) + adjust );
100 |           }
101 |           clickedArrow.style('color', activeColor);
102 |           otherArrow.style('color', defaultColor);
103 |           score.text(parseInt(score.text()) + adjust);
104 |           scoreDatum.voted = upvote ? 'upVote' : 'downVote';
105 |         } else {
106 |           clickedArrow.style('color', defaultColor);
107 |           score.text(parseInt(score.text()) - adjust);
108 |           scoreDatum.voted = 'none';
109 |         }
110 | 
111 |         scoreDatum.score = parseInt(score.text());
112 |         score.datum(scoreDatum);
113 |       } // end abstractVote()
114 | 
115 | 
116 |       function downVote(d) {
117 |         abstractVote(down, up);
118 | 
119 |         if (votingFns.downVote != undefined) votingFns.downVote(d);
120 |       }
121 |       function upVote(d) {
122 |         abstractVote(up, down);
123 | 
124 |         if (votingFns.upVote) votingFns.upVote(d);
125 |       }
126 | 
127 | 
128 |       var textStyle = {
129 |         color: '#fff',
130 |         display: 'inline-block',
131 |         'font-family': style.fontFamily,
132 |         'font-size': style.fontSize,
133 |         margin: '0px',
134 | 
135 |         // prevent selection
136 |         '-webkit-touch-callout': 'none',
137 |         '-webkit-user-select': 'none',
138 |         '-khtml-user-select': 'none',
139 |         '-moz-user-select': 'none',
140 |         '-ms-user-select': 'none',
141 |         'user-select': 'none'
142 |       }
143 |       down = selection.append('p')
144 |         .style(textStyle)
145 |         .style('padding', '0')
146 |         .style('cursor', 'pointer')
147 |         .text('▼')
148 |         .on('click', downVote);
149 |       score = selection.append('p')
150 |         .style(textStyle)
151 |         .style('padding', '0 1px 0 1px')
152 |         .text(data.score);
153 |       up = selection.append('p')
154 |         .style(textStyle)
155 |         .style('padding', '0')
156 |         .style('cursor', 'pointer')
157 |         .text('▲')
158 |         .on('click', upVote);
159 | 
160 |       if (score.datum().voted != undefined) {
161 |         if (score.datum().voted == 'upVote') up.style('color', activeColor);
162 |         if (score.datum().voted == 'downVote') down.style('color', activeColor);
163 |       }
164 |     }
165 | 
166 | 
167 |   // This function gets called whenever an element gets mouseovered
168 |   function activate (d) {
169 |     // Do nothing if no annotation data exists
170 |     if (d.annotation == undefined && d.cell.annotation == undefined) {
171 |       return;
172 |     }
173 | 
174 |     // Update annotation globals
175 |     target = target || d3.event.target;
176 |     svg = target.tagName.toLowerCase() == 'svg' ? target : target.ownerSVGElement;
177 |     if (d3.select(svg).select('SVGPoint').empty() == true) {
178 |       point = svg.createSVGPoint();
179 |     } else {
180 |       point = d3.select(svg).select('SVGPoint').node();
181 |     }
182 | 
183 | 
184 |     var aData = d.annotation || d.cell.annotation,
185 |         bbox = getScreenBBox();
186 | 
187 |     // Remove any lingering tooltips that might exist
188 |     d3.selectAll('.gd3AnnotationViewDiv').remove();
189 | 
190 |     // Create the new tooltip
191 |     var container = d3.select(document.createElement('div'));
192 |     container.attr('class', 'gd3AnnotationViewDiv');
193 |     container.style({
194 |       background: 'rgba(0,0,0,.75)',
195 |       'border-radius': '3px',
196 |       padding: '5px',
197 |       position: 'absolute'
198 |     });
199 | 
200 |     for (var i in aData) {
201 |       var aPart = aData[i],
202 |           type = aPart.type;
203 |       if (type == 'link') {
204 |         appendLink(container, aPart);
205 |       } else if (type == 'table') {
206 |         appendTable(container, aPart);
207 |       } else if (type == 'text') {
208 |         appendText(container, aPart);
209 |       }
210 |     }
211 | 
212 |     document.body.appendChild(container.node());
213 | 
214 |     // Determine positioning of the annotation
215 |     var node = container.node(),
216 |         scrollLeft = document.documentElement.scrollLeft || document.body.scrollLeft,
217 |         scrollTop = document.documentElement.scrollTop || document.body.scrollTop,
218 |         nodeL =  bbox.s.x - node.offsetWidth / 2,
219 |         nodeT = bbox.s.y;
220 | 
221 |     var offsetTop = nodeT + scrollTop + 2,
222 |         offsetLeft = nodeL + scrollLeft;
223 | 
224 |     container.style('left', offsetLeft.toString() + 'px')
225 |         .style('top', offsetTop.toString() + 'px');
226 | 
227 |     // Add an "x-out" button for the annotation
228 |     var xoutLeft = (node.offsetWidth - 10).toString() + 'px';
229 |     container.append('span')
230 |         .text('☓')
231 |         .on('click', function() {
232 |           d3.selectAll('.gd3AnnotationViewDiv').remove();
233 |         })
234 |         .style({
235 |           color: '#000',
236 |           cursor: 'pointer',
237 |           display: 'inline',
238 |           'font-size': '10px',
239 |           'font-weight': 'bold',
240 |           left: xoutLeft,
241 |           'line-height': 1,
242 |           position: 'absolute',
243 |           'text-align': 'right',
244 |           top: '-10px',
245 |           width: '10px'
246 |         });
247 | 
248 |     // container.on('mouseout', function() {
249 |     //   d3.select(this).on('mouseout', null); // patch for mouseout behavior
250 |     //   document.body.removeChild(this);
251 |     // });
252 |   }
253 | 
254 |     selection.on('mouseover', activate);
255 |   }
256 | 
257 |   return view;
258 | }


--------------------------------------------------------------------------------
/src/tooltip/index.js:
--------------------------------------------------------------------------------
 1 | import "tooltip";
 2 | 
 3 | import "tooltipElement";
 4 | 
 5 | import "tooltipImage";
 6 | import "tooltipText";
 7 | import "tooltipVote";
 8 | 
 9 | import "tooltipLink";
10 | import "tooltipTable";


--------------------------------------------------------------------------------
/src/tooltip/tooltip-license.md:
--------------------------------------------------------------------------------
 1 | The `gd3.tooltip()` component is based heavily on Justin Palmer's d3-tip add-on library (https://github.com/Caged/d3-tip), and as such we have included the MIT license specifically for this component.
 2 | 
 3 | The MIT License (MIT)
 4 | Copyright (c) 2013 Justin Palmer
 5 | 
 6 | Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 7 | 
 8 | The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
 9 | 
10 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.


--------------------------------------------------------------------------------
/src/tooltip/tooltip.js:
--------------------------------------------------------------------------------
 1 | import "tooltipStyle";
 2 | import "tooltipView";
 3 | 
 4 | ////////////////////////////////////////////////////////////////////////////////
 5 | // INFORMATION ABOUT GD3.TOOLTIP
 6 | //
 7 | // The gd3.tooltip() component is largely based on Justin Palmer's d3-tip
 8 | // plug-in (https://github.com/Caged/d3-tip). Lots and lots of thanks, Justin!
 9 | //
10 | // Differences:
11 | //   1. d3-tip is built such that only one tooltip can exist in a document,
12 | //        we altered this behavior, such that each call of gd3.tooltip() creates
13 | //        a brand new instance, meaning ∞ tooltips!
14 | //   2. to make making tooltips easier with complex data we've created a
15 | //        primitive type language for tooltip data that in turn lead to content
16 | //        factories that can automatically populate and format tooltips
17 | //
18 | 
19 | gd3.tooltip = {};
20 | 
21 | gd3.tooltip.make = function(params) {
22 |   var params = params || {},
23 |       style  = tooltipStyle(params.style || {}),
24 |       votingFns = params.votingFns || {};
25 | 
26 |   // annotation functions as a partial application, binding the given variables
27 |   //   into the returned instance.
28 |   return tooltipView(style);
29 | };
30 | 
31 | gd3.tooltip.data = function(ds) {
32 |   return ds.map(function(d) { return gd3.tooltip.datum(d); });
33 | }
34 | 
35 | // tooltip datum convenience constructor
36 | gd3.tooltip.datum = function(d) {
37 |   var elem = null;
38 |   if(!d.type) elem = new gd3.tooltip.text(d.toString());
39 |   else if(d.type == 'image') elem = new gd3.tooltip.image(d.src, d.title);
40 |   else if(d.type == 'link') elem = new gd3.tooltip.link(d.href, d.body);
41 |   else if(d.type == 'table') elem = new gd3.tooltip.table(d.table);
42 |   else if(d.type == 'text') elem = new gd3.tooltip.text(d.text);
43 |   else if(d.type == 'vote') elem = new gd3.tooltip.vote(d.downvoteFn, d.upvoteFn, d.voteCountFn, d.voteDirectionFn);
44 | 
45 |   if (elem == null) return new gd3.tooltip.text(d.toString());
46 |   return elem.showSummary(d.defaultHidden);
47 | }


--------------------------------------------------------------------------------
/src/tooltip/tooltipElement.js:
--------------------------------------------------------------------------------
 1 | gd3.tooltip.element = gd3_tooltipElement;
 2 | 
 3 | function gd3_tooltipElement() {
 4 | 
 5 | }
 6 | 
 7 | gd3_tooltipElement.prototype.summaryElement = false;
 8 | gd3_tooltipElement.prototype.showSummary = function(state) {
 9 |   state = state || false;
10 |   this.summaryElement = state;
11 |   return this;
12 | }


--------------------------------------------------------------------------------
/src/tooltip/tooltipImage.js:
--------------------------------------------------------------------------------
 1 | import "tooltipElement";
 2 | 
 3 | gd3.tooltip.image = gd3_tooltipImage;
 4 | 
 5 | function gd3_tooltipImage(src, title) {
 6 |   if (!this instanceof gd3_tooltipImage) return new gd3_tooltipImage(src, title);
 7 | 
 8 |   this.src = src;
 9 |   this.title = title;
10 |   this.type = "link";
11 |   return this;
12 | }
13 | 
14 | var gd3_tooltipImagePrototype = gd3_tooltipImage.prototype = new gd3_tooltipElement;
15 | 
16 | gd3_tooltipImagePrototype.toString = function() {
17 |   return this.title.toString();
18 | };
19 | 
20 | gd3_tooltipImagePrototype.render = function(selection) {
21 |   var thisTooltip = this;
22 |       img = selection.append('img')
23 |         .attr('src', this.src);
24 |   if(this.title) img.attr('alt', this.title);
25 | 
26 |   img.attr('data-summaryElement', this.summaryElement);
27 |   if(this.summaryElement) img.style('display', 'none');
28 |   return img;
29 | }


--------------------------------------------------------------------------------
/src/tooltip/tooltipLink.js:
--------------------------------------------------------------------------------
 1 | import "tooltipElement";
 2 | 
 3 | gd3.tooltip.link = gd3_tooltipLink;
 4 | 
 5 | function gd3_tooltipLink(href, body) {
 6 |   if (!this instanceof gd3_tooltipLink) return new gd3_tooltipLink(href, body);
 7 | 
 8 |   this.body = body;
 9 |   this.href = href;
10 |   this.type = "link";
11 |   return this;
12 | }
13 | 
14 | var gd3_tooltipLinkPrototype = gd3_tooltipLink.prototype = new gd3_tooltipElement;
15 | 
16 | gd3_tooltipLinkPrototype.toString = function() {
17 |   return this.body.toString();
18 | };
19 | 
20 | gd3_tooltipLinkPrototype.render = function(selection) {
21 |   var thisTooltip = this;
22 |       a = selection.append('a')
23 |       .attr('href', this.href);
24 | 
25 |   if (this.href[0] != '/') a.attr('target', '_new');
26 | 
27 |   if(thisTooltip.body.render) thisTooltip.body.render(a);
28 |   else a.text(thisTooltip.body.toString());
29 | 
30 |   a.attr('data-summaryElement', this.summaryElement);
31 |   if(this.summaryElement) a.style('display', 'none');
32 |   return a;
33 | }


--------------------------------------------------------------------------------
/src/tooltip/tooltipStyle.js:
--------------------------------------------------------------------------------
 1 | function tooltipStyle(style) {
 2 |   return {
 3 |     background: style.background || 'rgba(0, 0, 0, 0.75)',
 4 |     border: style.border || '1px solid rgba(0,0,0,0.8)',
 5 |     borderRadius: style.borderRadius || '2px',
 6 |     fontColor: style.fontColor || '#ffffff',
 7 |     fontFamily: style.fontFamily || '"HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif',
 8 |     fontSize: '11px',
 9 |     height: style.height || 200,
10 |     lineHeight: style.lineHeight || 1,
11 |     padding: style.padding || '5px',
12 |     voteActiveColor: style.voteActiveColor || '#ff0000',
13 |     width: style.width || 500,
14 |   };
15 | }


--------------------------------------------------------------------------------
/src/tooltip/tooltipTable.js:
--------------------------------------------------------------------------------
 1 | import "tooltipElement";
 2 | 
 3 | gd3.tooltip.table = gd3_tooltipTable;
 4 | 
 5 | // Array should be a 2D array.
 6 | function gd3_tooltipTable(array) {
 7 |   // TODO add a generator s.t. it makes 0-D array -> 1-D -> 2-D -> call gd3_tooltipTable(array)
 8 |   if (!this instanceof gd3_tooltipTable) return new gd3_tooltipTable(array);
 9 | 
10 |   this.table = array;
11 |   return this;
12 | }
13 | 
14 | var gd3_tooltipTablePrototype = gd3_tooltipTable.prototype = new gd3_tooltipElement;
15 | 
16 | gd3_tooltipTablePrototype.toString = function() {
17 |   return this.body.toString();
18 | };
19 | 
20 | gd3_tooltipTablePrototype.render = function(selection) {
21 |   var thisTooltip = this;
22 |       table = selection.append('table').attr('class', 'gd3-tooltip-table'),
23 |       rows = table.selectAll('tr').data(thisTooltip.table).enter().append('tr'),
24 |       cells = rows.selectAll('td').data(function(d) { return d; }).enter().append('td');
25 | 
26 |   cells.each(function(d){
27 |     if(d.render) d.render(d3.select(this));
28 |     else d3.select(this).text(d.toString());
29 |   });
30 | 
31 |   table.attr('data-summaryElement', this.summaryElement);
32 |   if(this.summaryElement) table.style('display', 'none');
33 |   return table;
34 | }


--------------------------------------------------------------------------------
/src/tooltip/tooltipText.js:
--------------------------------------------------------------------------------
 1 | import "tooltipElement";
 2 | 
 3 | gd3.tooltip.text = gd3_tooltipText;
 4 | 
 5 | function gd3_tooltipText(text) {
 6 |   if (!this instanceof gd3_tooltipText) return new gd3_tooltipText(text);
 7 | 
 8 |   this.text = text;
 9 |   this.type = "text";
10 |   return this;
11 | }
12 | 
13 | var gd3_tooltipTextPrototype = gd3_tooltipText.prototype = new gd3_tooltipElement;
14 | 
15 | gd3_tooltipTextPrototype.toString = function() {
16 |   return this.text;
17 | };
18 | 
19 | gd3_tooltipTextPrototype.render = function(selection) {
20 |   var text = selection.append('span').text(this.text);
21 |   text.attr('data-summaryElement', this.summaryElement);
22 |   if(this.summaryElement) text.style('display', 'none');
23 |   else text.style('display', 'block');
24 |   return text;
25 | }


--------------------------------------------------------------------------------
/src/tooltip/tooltipView.js:
--------------------------------------------------------------------------------
  1 | function tooltipView(style) {
  2 |   var clickCount = 0,
  3 |       clickEvents = {},
  4 |       direction = d3_tip_direction,
  5 |       offset    = d3_tip_offset,
  6 |       html      = d3_tip_html,
  7 |       node      = undefined,
  8 |       sticky    = false,
  9 |       svg       = null,
 10 |       point     = null,
 11 |       target    = null;
 12 | 
 13 | 
 14 |   function positionTooltip() {
 15 |       var args = Array.prototype.slice.call(arguments)
 16 | 
 17 |       // Obtain location information
 18 |       var poffset = offset.apply(this, args),
 19 |           coords,
 20 |           dir     = direction.apply(this, args),
 21 |           i       = directions.length,
 22 |           nodel = d3.select(node),
 23 |           scrollTop  = document.documentElement.scrollTop || document.body.scrollTop,
 24 |           scrollLeft = document.documentElement.scrollLeft || document.body.scrollLeft;
 25 | 
 26 |       while(i--) nodel.classed(directions[i], false);
 27 |       coords = direction_callbacks.get(dir).apply(this);
 28 |       nodel.classed(dir, true).style({
 29 |         top: (coords.top +  poffset[0]) + scrollTop + 'px',
 30 |         left: (coords.left + poffset[1]) + scrollLeft + 'px'
 31 |       });
 32 |     }
 33 | 
 34 |   function view(selection) {
 35 |     svg = selection; // assumes selection is an SVG
 36 |     point = selection.node().createSVGPoint();
 37 | 
 38 |     // node = d3.select(document.createElement('div'));
 39 |     node = d3.select('body').append('div');
 40 |     node.attr('class','gd3-tooltip')
 41 |     node.style({
 42 |       background: style.background,
 43 |       border: style.border,
 44 |       'border-radius': style.borderRadius,
 45 |       color: style.fontColor,
 46 |       'font-family': style.fontFamily,
 47 |       'font-size': style.fontSize,
 48 |       'line-height': style.lineHeight,
 49 |       overflow: 'hidden',
 50 |       position: 'absolute',
 51 |       top: 0,
 52 |       opacity: 0,
 53 |       'pointer-events': 'none',
 54 |       'box-sizing': 'border-box',
 55 |       padding: style.padding
 56 |     });
 57 |     node = node.node();
 58 | 
 59 |     // Create a listener for the body to close on keypress (ESC)
 60 |     var uniqueID = Date.now();
 61 |     d3.select('body').on('keydown.gd3-tooltip-exit-'+uniqueID, function() {
 62 |       if (d3.event.keyCode == 27) {
 63 |         sticky = false;
 64 |         view.hide();
 65 |       }
 66 |     });
 67 | 
 68 |     var tipObjects = selection.selectAll('.gd3-tipobj')
 69 |         .on('click', function() {
 70 |             sticky = sticky ? false : true;
 71 |             if(sticky) {
 72 |               // view.render();
 73 |               if(d3.event.type != 'click') return;
 74 |                 d3.select(node).selectAll('*').each(function() {
 75 |                   var thisEl = d3.select(this),
 76 |                       isSummaryElement = thisEl.attr('data-summaryElement');
 77 |                   if(isSummaryElement) thisEl.style('display', 'block');
 78 |                 });
 79 |                 positionTooltip();
 80 |               }
 81 |             else view.hide();
 82 |         })
 83 |         .on('mouseover', view.render )
 84 |         .on('mouseout', view.hide );
 85 |   } // end view
 86 | 
 87 |   view.render = function() {
 88 |     // if the node is sticky (i.e., has been clicked, or otherwise frozen)
 89 |     if (sticky) {
 90 |       // If the event isn't a click event, don't do anything
 91 |       if(d3.event.type != 'click') return;
 92 | 
 93 |       d3.select(node).selectAll('*').each(function() {
 94 |         var thisEl = d3.select(this),
 95 |             isSummaryElement = thisEl.attr('data-summaryElement');
 96 |         if(isSummaryElement) thisEl.style('display', 'block');
 97 |       });
 98 |       positionTooltip();
 99 |       return;
100 |     }
101 | 
102 |     var args = Array.prototype.slice.call(arguments);
103 |     if(args[args.length - 1] instanceof SVGElement) target = args.pop();
104 | 
105 | 
106 |     var content = html.apply(this, args),
107 |         nodel   = d3.select(node);
108 | 
109 |     var xout = '<span class="gd3-tooltip-xout" style="cursor: pointer; float: right; font-size:8px;">X</span><br/>';
110 |     nodel.html(xout);
111 | 
112 |     content.forEach(function(tipElem) {
113 |       tipElem.render(nodel);
114 |     });
115 |     nodel.style({ opacity: 1, 'pointer-events': 'all' });
116 | 
117 |     nodel.select('.gd3-tooltip-xout')
118 |       .on('click', function () {
119 |         // Activate tipObejcts.on('click') and tipObjects.on('mouseover')
120 |         sticky = sticky ? false : true;
121 |         view.hide();
122 |       });
123 | 
124 |     var clickEventObjs = nodel.selectAll('.clickEventObj');
125 |     if (clickEventObjs.empty() == false) {
126 |       clickEventObjs.each(function() {
127 |         var thisEl = d3.select(this),
128 |             clickIndex = thisEl.attr('data-click'),
129 |             clickEvent = clickEvents[clickIndex];
130 |         thisEl.on('click', clickEvent);
131 |       });
132 |     }
133 | 
134 |     positionTooltip();
135 | 
136 |     return view;
137 |   }
138 | 
139 |   view.hide = function() {
140 |     if (sticky) return;
141 |     var nodel = d3.select(node);
142 |     nodel.style({ opacity: 0, 'pointer-events': 'none' });
143 | 
144 |     d3.select(node).selectAll('*').each(function() {
145 |         var thisEl = d3.select(this),
146 |             isSummaryElement = thisEl.attr('data-summaryElement');
147 |         if(isSummaryElement) thisEl.style('display', 'none');
148 |       });
149 |     return view;
150 |   }
151 | 
152 |   view.attr = function(n, v) {
153 |     if (arguments.length < 2 && typeof n === 'string') {
154 |       return d3.select(node).attr(n)
155 |     } else {
156 |       var args =  Array.prototype.slice.call(arguments)
157 |       d3.selection.prototype.attr.apply(d3.select(node), args)
158 |     }
159 | 
160 |     return view;
161 |   }
162 | 
163 |   view.style = function(n, v) {
164 |     if (arguments.length < 2 && typeof n === 'string') {
165 |       return d3.select(node).style(n)
166 |     } else {
167 |       var args =  Array.prototype.slice.call(arguments)
168 |       d3.selection.prototype.style.apply(d3.select(node), args)
169 |     }
170 | 
171 |     return view;
172 |   }
173 | 
174 |   view.direction = function(v) {
175 |     if (!arguments.length) return direction
176 |     direction = v == null ? v : d3.functor(v)
177 | 
178 |     return view;
179 |   }
180 | 
181 |   view.offset = function(v) {
182 |     if (!arguments.length) return offset
183 |     offset = v == null ? v : d3.functor(v)
184 | 
185 |     return view;
186 |   }
187 | 
188 |   view.html = function(v) {
189 |     if (!arguments.length) return html
190 |     html = v == null ? v : d3.functor(v)
191 | 
192 |     return view;
193 |   }
194 | 
195 |   // use the given data to generate an HTML string and proceed as normal
196 |   view.useData = function(data) {
197 |     function depth(d) {
198 |       return Array.isArray(d) ? depth(d[0])+1 : 0;
199 |     }
200 | 
201 |     var ghostNode = document.createElement('div'),
202 |         nodel = d3.select(ghostNode);
203 | 
204 |     var dimensionality = depth(data);
205 | 
206 |     function registerClickEvent(selection) {
207 |       if(selection.on('click')) {
208 |         selection.attr('data-click', clickCount).classed('clickEventObj', true);
209 |         clickEvents[clickCount] = selection.on('click');
210 |         clickCount = clickCount + 1;
211 |       }
212 |     }
213 | 
214 |     // Alter the rendering behavior based on the dimensionality of data
215 |     if(dimensionality == 0) {
216 |       html = d3.functor([data]);
217 |     } else if (dimensionality == 1) {
218 |       html = d3.functor(data);
219 |     } else {
220 |       html = d3.functor(function(d,i) {return data[i]; });
221 |     }
222 | 
223 |     return view;
224 |   }
225 | 
226 |   //////////////////////////////////////////////////////////////////////////////////////////////////
227 |   // Private functions
228 | 
229 |   // Create functions for determining which direction the tip should render
230 |   function d3_tip_direction() { return 'n' }
231 |   function d3_tip_offset() { return [0, 0] }
232 |   function d3_tip_html() { return ' ' }
233 | 
234 |   var direction_callbacks = d3.map({
235 |     n:  direction_n,
236 |     s:  direction_s,
237 |     e:  direction_e,
238 |     w:  direction_w,
239 |     nw: direction_nw,
240 |     ne: direction_ne,
241 |     sw: direction_sw,
242 |     se: direction_se
243 |   }),
244 | 
245 |   directions = direction_callbacks.keys();
246 | 
247 |   function direction_n() {
248 |     var bbox = getScreenBBox();
249 |     return {
250 |       top:  bbox.n.y - node.offsetHeight,
251 |       left: bbox.n.x - node.offsetWidth / 2
252 |     }
253 |   }
254 | 
255 |   function direction_s() {
256 |     var bbox = getScreenBBox();
257 |     return {
258 |       top:  bbox.s.y,
259 |       left: bbox.s.x - node.offsetWidth / 2
260 |     }
261 |   }
262 | 
263 |   function direction_e() {
264 |     var bbox = getScreenBBox();
265 |     return {
266 |       top:  bbox.e.y - node.offsetHeight / 2,
267 |       left: bbox.e.x
268 |     }
269 |   }
270 | 
271 |   function direction_w() {
272 |     var bbox = getScreenBBox();
273 |     return {
274 |       top:  bbox.w.y - node.offsetHeight / 2,
275 |       left: bbox.w.x - node.offsetWidth
276 |     }
277 |   }
278 | 
279 |   function direction_nw() {
280 |     var bbox = getScreenBBox();
281 |     return {
282 |       top:  bbox.nw.y - node.offsetHeight,
283 |       left: bbox.nw.x - node.offsetWidth
284 |     }
285 |   }
286 | 
287 |   function direction_ne() {
288 |     var bbox = getScreenBBox();
289 |     return {
290 |       top:  bbox.ne.y - node.offsetHeight,
291 |       left: bbox.ne.x
292 |     }
293 |   }
294 | 
295 |   function direction_sw() {
296 |     var bbox = getScreenBBox();
297 |     return {
298 |       top:  bbox.sw.y,
299 |       left: bbox.sw.x - node.offsetWidth
300 |     }
301 |   }
302 | 
303 |   function direction_se() {
304 |     var bbox = getScreenBBox();
305 |     return {
306 |       top:  bbox.se.y,
307 |       left: bbox.e.x
308 |     }
309 |   }
310 | 
311 |   // Private - gets the screen coordinates of a shape
312 |   //
313 |   // Given a shape on the screen, will return an SVGPoint for the directions
314 |   // n(north), s(south), e(east), w(west), ne(northeast), se(southeast), nw(northwest),
315 |   // sw(southwest).
316 |   //
317 |   //    +-+-+
318 |   //    |   |
319 |   //    +   +
320 |   //    |   |
321 |   //    +-+-+
322 |   //
323 |   // Returns an Object {n, s, e, w, nw, sw, ne, se}
324 |   function getScreenBBox() {
325 |     var targetel   = target || d3.event.target;
326 | 
327 |     while ('undefined' === typeof targetel.getScreenCTM && 'undefined' === targetel.parentNode) {
328 |         targetel = targetel.parentNode;
329 |     }
330 | 
331 |     var bbox       = {},
332 |         matrix     = targetel.getScreenCTM(),
333 |         tbbox      = targetel.getBBox(),
334 |         width      = tbbox.width,
335 |         height     = tbbox.height,
336 |         x          = tbbox.x,
337 |         y          = tbbox.y
338 | 
339 |     point.x = x
340 |     point.y = y
341 |     bbox.nw = point.matrixTransform(matrix)
342 |     point.x += width
343 |     bbox.ne = point.matrixTransform(matrix)
344 |     point.y += height
345 |     bbox.se = point.matrixTransform(matrix)
346 |     point.x -= width
347 |     bbox.sw = point.matrixTransform(matrix)
348 |     point.y -= height / 2
349 |     bbox.w  = point.matrixTransform(matrix)
350 |     point.x += width
351 |     bbox.e = point.matrixTransform(matrix)
352 |     point.x -= width / 2
353 |     point.y -= height / 2
354 |     bbox.n = point.matrixTransform(matrix)
355 |     point.y += height
356 |     bbox.s = point.matrixTransform(matrix)
357 | 
358 |     return bbox
359 |   }
360 | 
361 |   // end private functions
362 |   //////////////////////////////////////////////////////////////////////////////////////////////////
363 | 
364 |   return view;
365 | }


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/src/tooltip/tooltipVote.js:
--------------------------------------------------------------------------------
  1 | import "tooltipElement";
  2 | 
  3 | gd3.tooltip.vote = gd3_tooltipVote;
  4 | var gd3_tooltipVotePrototype = gd3_tooltipVote.prototype = new gd3_tooltipElement;
  5 | 
  6 | function gd3_tooltipVote(downvoteFn, upvoteFn, voteCountFn, voteDirectionFn) {
  7 |   if (!this instanceof gd3_tooltipVote) {
  8 |     return new gd3_tooltipVote(downvoteFn, upvoteFn, voteCountFn, voteDirectionFn);
  9 |   }
 10 | 
 11 |   this.downvoteFn = downvoteFn;
 12 |   this.upvoteFn = upvoteFn;
 13 |   this.voteCountFn = voteCountFn;
 14 |   this.voteDirectionFn = voteDirectionFn;
 15 | 
 16 |   return this;
 17 | }
 18 | 
 19 | gd3_tooltipVotePrototype.toString = function() {
 20 |   if (typeof(this.voteCount) == 'function') return this.voteCount() + ' votes';
 21 |   return this.voteCount + ' votes';
 22 | };
 23 | 
 24 | gd3_tooltipVotePrototype.render = function(selection) {
 25 |   var votingArea = selection.append('span').attr('class', 'gd3-tooltip-vote'),
 26 |       downVote = votingArea.append('span').text('▼').attr('class', 'gd3-tooltip-dvote'),
 27 |       upVote = votingArea.append('span').text('▲').attr('class', 'gd3-tooltip-uvote'),
 28 |       voteCount = votingArea.append('span')
 29 |         .attr('class', 'gd3-tooltip-votecount')
 30 |         .text(this.voteCountFn());
 31 | 
 32 |   if(this.voteDirectionFn) {
 33 |     if (this.voteDirectionFn() == "down") {
 34 |       downVote.classed("gd3-vote-active", true);
 35 |       downVote.style("color", "goldenrod");
 36 |     } else if (this.voteDirectionFn() == "up") {
 37 |       upVote.classed("gd3-vote-active", true);
 38 |       upVote.style("color", "goldenrod");
 39 |     }
 40 |   }
 41 | 
 42 |   votingArea.style('display', 'block');
 43 |   votingArea.selectAll('span').style({
 44 |     display: 'inline-block'
 45 |   });
 46 | 
 47 |   var downVoteFn = this.downVoteFn,
 48 |       thisVote = this;
 49 | 
 50 |   downVote.on('click', function(d) {
 51 |     // vote elements need to be redefined because of the way element rendering currently works
 52 |     var downVote = d3.select(this),
 53 |         upVote = d3.select(this.parentNode).select('.gd3-tooltip-uvote'),
 54 |         voteCount = d3.select(this.parentNode).select('.gd3-tooltip-votecount');
 55 | 
 56 |     upVote.style('color', null);
 57 | 
 58 |     // Do nothing if the vote is already active
 59 |     if (downVote.classed('gd3-vote-active') == true) {
 60 |       downVote.classed('gd3-vote-active', false);
 61 |       downVote.style('color', null);
 62 |     } else {
 63 |       // Alter classes
 64 |       downVote.classed('gd3-vote-active', true);
 65 |       upVote.classed('gd3-vote-active', false);
 66 | 
 67 |       // Style downvote
 68 |       downVote.style('color', 'goldenrod');
 69 |     }
 70 | 
 71 |     // Vote function always functions on click and passes current state
 72 |     var vote = thisVote.downvoteFn(d, downVote.classed('gd3-vote-active'));
 73 |     if (vote){
 74 |       upVote.classed('gd3-vote-active', false);
 75 |       downVote.classed('gd3-vote-active', true);
 76 |     }
 77 |     voteCount.text( voteCount.datum().voteCountFn() );
 78 |   });
 79 | 
 80 | 
 81 |   upVote.on('click', function(d) {
 82 |     // vote elements need to be redefined because of the way element rendering currently works
 83 |     var downVote = d3.select(this.parentNode).select('.gd3-tooltip-dvote'),
 84 |         upVote = d3.select(this),
 85 |         voteCount = d3.select(this.parentNode).select('.gd3-tooltip-votecount');
 86 | 
 87 |     downVote.style('color', null);
 88 | 
 89 |     if (upVote.classed('gd3-vote-active') == true) {
 90 |       upVote.classed('gd3-vote-active', false);
 91 |       upVote.style('color', null);
 92 |     } else {
 93 |       // Alter classes
 94 |       downVote.classed('gd3-vote-active', false);
 95 |       upVote.classed('gd3-vote-active', true);
 96 | 
 97 |       // Style upvote
 98 |       upVote.style('color', 'goldenrod');
 99 |     }
100 | 
101 | 
102 |     // Vote function always functions on click and passes current state
103 |     var vote = thisVote.upvoteFn(d, upVote.classed('gd3-vote-active'));
104 |     if (vote){
105 |       downVote.classed('gd3-vote-active', false);
106 |       upVote.classed('gd3-vote-active', true);
107 |     }
108 |     voteCount.text( voteCount.datum().voteCountFn() );
109 |   });
110 | 
111 | 
112 |   var voteGlyphStyle = {
113 |     cursor: 'pointer',
114 |     '-moz-user-select': 'none',
115 |     '-ms-user-select': 'none',
116 |     '-o-user-select': 'none',
117 |     '-webkit-user-select': 'none'
118 |   }
119 | 
120 |   downVote.style(voteGlyphStyle);
121 |   upVote.style(voteGlyphStyle);
122 | 
123 |   votingArea.attr('data-summaryElement', this.summaryElement);
124 |   if(this.summaryElement) votingArea.style('display', 'none');
125 |   return votingArea;
126 | }


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/src/transcript/index.js:
--------------------------------------------------------------------------------
1 | import "transcript";


--------------------------------------------------------------------------------
/src/transcript/transcript.js:
--------------------------------------------------------------------------------
 1 | import "transcriptChart";
 2 | import "transcriptStyle";
 3 | 
 4 | gd3.transcript = function(params) {
 5 |   var params = params || {},
 6 |       style  = transcriptStyle(params.style || {});
 7 | 
 8 |   // transcriptChart functions as a partial application, binding the given variables
 9 |   //   into the returned instance.
10 |   return transcriptChart(style);
11 | };


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/src/transcript/transcriptData.js:
--------------------------------------------------------------------------------
  1 | function transcriptData(data) {
  2 |   function parseCancer(cdata) {
  3 |     var defaultInactivatingMutations = {
  4 |           "Nonsense_Mutation": true,
  5 |           "Frame_Shift_Del": true,
  6 |           "Frame_Shift_Ins":true,
  7 |           "Missense_Mutation": false,
  8 |           "Splice_Site": true,
  9 |           "In_Frame_Del": false,
 10 |           "In_Frame_Ins": false
 11 |         };
 12 |     var defaultMutationTypesToSymbols = {
 13 |           "Nonsense_Mutation": 0,
 14 |           "Frame_Shift_Del": 1,
 15 |           "Frame_Shift_Ins": 1,
 16 |           "Missense_Mutation": 2,
 17 |           "Splice_Site": 3,
 18 |           "In_Frame_Del": 4,
 19 |           "In_Frame_Ins": 4
 20 |         };
 21 | 
 22 |     // Select the initial protein domain db, going with the first one
 23 |     // if it's not provided. Then add the protein domain dbs to each of the domains
 24 |     // so we can easily toggle through the different databases 
 25 |     var proteinDomainDB = cdata.proteinDomainDB || Object.keys(cdata.domains)[0] || '';
 26 |     var domains = [];
 27 |     Object.keys(cdata.domains).forEach(function(db){
 28 |       cdata.domains[db].forEach(function(d){
 29 |         d.db = db;
 30 |         domains.push(d);
 31 |       });
 32 |     });
 33 | 
 34 |     var d = {
 35 |       geneName: cdata.gene,
 36 |       sequence: cdata.protein_sequence || null,
 37 |       sequence_annotations: cdata.sequence_annotations || [],
 38 |       inactivatingMutations: cdata.inactivatingMutations || defaultInactivatingMutations,
 39 |       length: cdata.length,
 40 |       mutationCategories: cdata.mutationCategories || [],
 41 |       mutations: cdata.mutations,
 42 |       mutationTypesToSymbols: cdata.mutationTypesToSymbols || defaultMutationTypesToSymbols,
 43 |       proteinDomainDB: proteinDomainDB,
 44 |       proteinDomains: domains || []
 45 |     };
 46 |     d.types = Object.keys(d.mutationTypesToSymbols);
 47 |     d.datasets = d3.set(cdata.mutations.map(function(m) { return m.dataset; })).values();
 48 |     d.locusToAnnotations = {};
 49 |     var seq_annotation_types = d3.set();
 50 |     d.sequence_annotations.forEach(function(anno){
 51 |       d.locusToAnnotations[anno.locus] = anno.annotation;
 52 |       seq_annotation_types.add(anno.annotation);
 53 |     });
 54 |     d.seq_annotation_types = seq_annotation_types.values().sort();
 55 | 
 56 |     // for (var mutation in d.mutations) {
 57 |     //   var m = d.mutations[mutation];
 58 | 
 59 |     //   // create simulated annotation data if it does not exist.
 60 |     //   if (m.annotation == undefined) {
 61 |     //     var vote = {
 62 |     //       type: 'vote',
 63 |     //       score: 100
 64 |     //     }
 65 |     //     var link = {
 66 |     //       type: 'link',
 67 |     //       href: 'http://www.cs.brown.edu',
 68 |     //       text: 'BrownCS'
 69 |     //     }
 70 |     //     m.annotation = [
 71 |     //       {
 72 |     //         type: 'text',
 73 |     //         title: 'Sample',
 74 |     //         text: m.sample
 75 |     //       },
 76 |     //       {
 77 |     //         type: 'table',
 78 |     //         header: ['Cancer', 'PMIDs', 'Votes'],
 79 |     //         data: [
 80 |     //           ['1', link, vote],
 81 |     //           ['4', link, vote]
 82 |     //         ]
 83 |     //       }
 84 |     //     ];
 85 |     //   } // end simulated m.annotation
 86 |     //   else {
 87 |     //     console.log('defined annotation');
 88 |     //   }
 89 |     // }
 90 | 
 91 |     d.get = function(str) {
 92 |       if (str == 'length') return d.length;
 93 |       else if (str == 'datasets') return d.datasets;
 94 |       else if (str == 'mutations') return d.mutations;
 95 |       else if (str == 'mutationTypesToSymbols') return d.mutationTypesToSymbols;
 96 |       else if (str == 'proteinDomains') return d.proteinDomains;
 97 |       else if (str == 'sequence') return d.sequence;
 98 |       else return null;
 99 |     }
100 |     d.isMutationInactivating = function(mut) {
101 |       return d.inactivatingMutations[mut];
102 |     }
103 |     // Find the first domain that includes the given locus
104 |     d.domain = function(locus){
105 |       var loc = locus * 1; // convert to integer
106 |       for (var i = 0; i < d.proteinDomains.length; i++){
107 |         if (d.proteinDomains[i].start < loc && d.proteinDomains[i].end > loc){
108 |           return d.proteinDomains[i].name;
109 |         }
110 |       }
111 |       return null;
112 |     }
113 | 
114 |     return d;
115 |   }
116 |   var tData = parseCancer(data);
117 | 
118 |   return tData;
119 | }
120 | 


--------------------------------------------------------------------------------
/src/transcript/transcriptStyle.js:
--------------------------------------------------------------------------------
 1 | function transcriptStyle(style) {
 2 |   return {
 3 |     fontFamily: '"HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif',
 4 |     height: style.height || 250,
 5 |     numXTicks: style.numXTicks || 5,
 6 |     symbolWidth: style.symbolWidth || 20,
 7 |     transcriptBarHeight: style.transcriptBarHeight || 20,
 8 |     legendSymbolHeight: style.legendSymbolHeight || 14,
 9 |     width: style.width || 500,
10 |     xTickPadding: style.xTickPadding || 1.25,
11 |     scollbarWidth: style.scrollbarWidth || 15,
12 |     legendTextWidth: style.legendTextWidth || 28,
13 |     margin: style.margin || { left: 5, right: 15, top: 5, bottom: 0 },
14 |     seqAnnotationColors: {Phosphorylation: '#ff0000', Acetylation: '#00ff00', Ubiquitination: '#0000ff', Regulatory: 'rgb(44, 160, 44)', Methylation: 'rgb(255, 127, 14)', "Disease-associated": 'rgb(31, 119, 180)'}
15 |   };
16 | }


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/test/placeholder.md:
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https://raw.githubusercontent.com/raphael-group/gd3/44657c87ddc5a6b465617470ef58a01787fae85e/test/placeholder.md


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