Merge pull request #22 from nicgirault/v2

V2
nicgirault · Mar 8, 2017 · fa61880 · fa61880
2 parents 047a71c + 64413c7
commit fa61880
Show file tree

Hide file tree

Showing 233 changed files with 111,506 additions and 17,412 deletions.
diff --git a/.babelrc b/.babelrc
@@ -0,0 +1,3 @@
+{
+  "presets": ["es2015"]
+}
diff --git a/.eslintrc b/.eslintrc
@@ -0,0 +1,6 @@
+{
+  "extends": "google",
+  "parser": "babel-eslint",
+  "rules": {
+  }
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,2 @@
+Collision between ids
+Rules => faire des callbacks à la place
diff --git a/bower.json b/bower.json
@@ -1,7 +1,7 @@
 {
   "name": "circosjs",
   "description": "d3js library to draw circular graphs",
-  "main": "dist/circosJS.js",
+  "main": "dist/circos.min.js",
   "license": "GPL-2.0",
   "ignore": [
     "demo"
@@ -34,11 +34,7 @@
     "url": "git://nicgirault/circosJS.git"
   },
   "dependencies": {
-    "d3": "~3.5.2",
-    "colorBrewer": "https://raw.githubusercontent.com/d3/d3/bower-metadata/lib/colorbrewer/colorbrewer.css",
-    "d3-tip": "~0.6.8"
   },
   "resolutions": {
-    "d3": "~3.5.2"
   }
 }
diff --git a/demo/chords/index.html b/demo/chords/index.html
@@ -0,0 +1,16 @@
+<!DOCTYPE html>
+<html lang='en'>
+
+<head>
+    <title>circosJS</title>
+    <meta charset='utf-8'></meta>
+    <script src='../../dist/circos.js'></script>
+    <script src='https://cdnjs.cloudflare.com/ajax/libs/d3/4.5.0/d3.js'></script>
+    <script src='https://cdnjs.cloudflare.com/ajax/libs/d3-queue/3.0.3/d3-queue.js'></script>
+</head>
+
+<body>
+    <div id='chart'></div>
+    <script src='./index.js'></script>
+</body>
+</html>
diff --git a/demo/chords/index.js b/demo/chords/index.js
@@ -0,0 +1,93 @@
+var gieStainColor = {
+  gpos100: 'rgb(0,0,0)',
+  gpos: 'rgb(0,0,0)',
+  gpos75: 'rgb(130,130,130)',
+  gpos66: 'rgb(160,160,160)',
+  gpos50: 'rgb(200,200,200)',
+  gpos33: 'rgb(210,210,210)',
+  gpos25: 'rgb(200,200,200)',
+  gvar: 'rgb(220,220,220)',
+  gneg: 'rgb(255,255,255)',
+  acen: 'rgb(217,47,39)',
+  stalk: 'rgb(100,127,164)',
+  select: 'rgb(135,177,255)',
+};
+
+var drawCircos = function(error, GRCh37, cytobands, data) {
+  var circos = new Circos({
+    container: '#chart',
+    width: 1000,
+    height: 1050,
+  });
+
+  cytobands = cytobands.map(function(d) {
+    return {
+      block_id: d.chrom,
+      start: parseInt(d.chromStart),
+      end: parseInt(d.chromEnd),
+      gieStain: d.gieStain,
+      name: d.name,
+    };
+  });
+
+  data = data.map(function(d) {
+    return {
+      source: {
+        id: d.source_id,
+        start: parseInt(d.source_breakpoint) - 2000000,
+        end: parseInt(d.source_breakpoint) + 2000000,
+      },
+      target: {
+        id: d.target_id,
+        start: parseInt(d.target_breakpoint) - 2000000,
+        end: parseInt(d.target_breakpoint) + 2000000,
+      },
+    };
+  });
+
+  circos
+    .layout(
+      GRCh37,
+      {
+        innerRadius: 400,
+        outerRadius: 440,
+        labels: {
+          radialOffset: 70,
+        },
+        ticks: {
+          display: true,
+          labelDenominator: 1000000,
+        },
+      }
+    )
+    .highlight('cytobands', cytobands, {
+      innerRadius: 400,
+      outerRadius: 440,
+      opacity: 0.3,
+      color: function(d) {
+        return gieStainColor[d.gieStain];
+      },
+      tooltipContent: function(d) {
+        return d.name;
+      },
+    })
+    .chords(
+      'l1',
+      data,
+      {
+        logScale: false,
+        opacity: 0.7,
+        color: '#ff5722',
+        tooltipContent: function(d) {
+          return d.source.id + ' ➤ ' + d.target.id + ': ' + d.value;
+        },
+      }
+    )
+    .render();
+};
+
+d3.queue()
+  .defer(d3.json, '../data/GRCh37.json')
+  .defer(d3.csv, '../data/cytobands.csv')
+  .defer(d3.csv, '../data/fusion-genes.csv')
+  .await(drawCircos);
diff --git a/demo/data/GRCh37.json b/demo/data/GRCh37.json
@@ -0,0 +1,26 @@
+[
+  {"id":"chr1","label":"chr1","color":"#996600","len":249250621},
+  {"id":"chr2","label":"chr2","color":"#666600","len":243199373},
+  {"id":"chr3","label":"chr3","color":"#99991E","len":198022430},
+  {"id":"chr4","label":"chr4","color":"#CC0000","len":191154276},
+  {"id":"chr5","label":"chr5","color":"#FF0000","len":180915260},
+  {"id":"chr6","label":"chr6","color":"#FF00CC","len":171115067},
+  {"id":"chr7","label":"chr7","color":"#FFCCCC","len":159138663},
+  {"id":"chr8","label":"chr8","color":"#FF9900","len":146364022},
+  {"id":"chr9","label":"chr9","color":"#FFCC00","len":141213431},
+  {"id":"chr10","label":"chr10","color":"#FFFF00","len":135534747},
+  {"id":"chr11","label":"chr11","color":"#CCFF00","len":135006516},
+  {"id":"chr12","label":"chr12","color":"#00FF00","len":133851895},
+  {"id":"chr13","label":"chr13","color":"#358000","len":115169878},
+  {"id":"chr14","label":"chr14","color":"#0000CC","len":107349540},
+  {"id":"chr15","label":"chr5","color":"#6699FF","len":102531392},
+  {"id":"chr16","label":"chr16","color":"#99CCFF","len":90354753},
+  {"id":"chr17","label":"chr17","color":"#00FFFF","len":81195210},
+  {"id":"chr18","label":"chr18","color":"#CCFFFF","len":78077248},
+  {"id":"chr19","label":"chr19","color":"#9900CC","len":59128983},
+  {"id":"chr20","label":"chr20","color":"#CC33FF","len":63025520},
+  {"id":"chr21","label":"chr21","color":"#CC99FF","len":48129895},
+  {"id":"chr22","label":"chr22","color":"#666666","len":51304566},
+  {"id":"chrX","label":"chrX","color":"#999999","len":155270560},
+  {"id":"chrY","label":"chrY","color":"#CCCCCC","len":59373566}
+]
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Collision between ids
		Rules => faire des callbacks à la place