{"action":"created","comment":{"url":"https://api.github.com/repos/ViDA-NYU/genotet/pulls/comments/46246660","id":46246660,"diff_hunk":"@@ -244,180 +413,341 @@ genotet.ExpressionRenderer.prototype.drawGeneProfiles_ = function() {\n     this.svgProfile_.selectAll('*').remove();\n     return;\n   }\n+  else if (!this.data.options.showGeneLabels) {\n+    this.PROFILE_MARGINS.LEFT = this.DEFAULT_PROFILE_MARGIN;\n+  }\n+  else {\n+    this.PROFILE_MARGINS.LEFT = this.geneLabelWidth_ + this.LABEL_MARGIN_;\n+  }\n+\n+  var heatmapData = this.data.matrix;\n+  this.svgProfile_.selectAll('g').remove();\n+  this.svgProfile_.attr('width', this.canvasWidth_);\n+\n+  var xScale = d3.scale.linear().range([\n+    this.PROFILE_MARGINS.LEFT,\n+    this.canvasWidth_ - this.PROFILE_MARGINS.RIGHT\n+  ]).domain([0, heatmapData.conditionNames.length - 1]);\n+  var yScale = d3.scale.linear().range([\n+    this.profileHeight_ - this.PROFILE_MARGINS.BOTTOM,\n+    this.PROFILE_MARGINS.TOP\n+  ]).domain([heatmapData.valueMin, heatmapData.valueMax]);\n+  var xAxis = d3.svg.axis()\n+    .scale(xScale).orient('bottom');\n+  var yAxis = d3.svg.axis()\n+    .scale(yScale).orient('left');\n+  this.svgProfile_\n+    .append('svg:g').call(xAxis)\n+    .classed('axis', true)\n+    .classed('x', true)\n+    .attr(\n+      'transform',\n+      'translate(0, ' + (this.profileHeight_ - this.PROFILE_MARGINS.BOTTOM) + ')'\n+    );\n+  this.svgProfile_\n+    .append('svg:g').call(yAxis)\n+    .classed('axis', true)\n+    .attr('transform', 'translate(' + this.PROFILE_MARGINS.LEFT + ', 0)');\n+\n+  var colors = d3.scale.category20()\n+    .range()\n+    .concat(d3.scale.category20b().range())\n+    .concat(d3.scale.category20c().range());\n+  var profileContent = this.svgProfile_.append('g')\n+    .attr(\n+      'width',\n+      this.canvasWidth_ - this.PROFILE_MARGINS.LEFT - this.PROFILE_MARGINS.RIGHT\n+    )\n+    .attr(\n+      'height',\n+      this.profileHeight_ - this.PROFILE_MARGINS.TOP - this.PROFILE_MARGINS.BOTTOM\n+    );\n+\n+  var line = d3.svg.line()\n+    .x(function(data, i) {\n+      return xScale(i);\n+    })\n+    .y(function(data) {\n+      return yScale(data);\n+    })\n+    .interpolate('linear');\n+  this.data.profiles.forEach(function(path, i) {\n+    var geneIndex = this.data.profiles[i].row;\n+    var pathColor = colors[genotet.utils.hashString(heatmapData.geneNames[geneIndex]) % 60];\n+    this.data.profiles[i] = {\n+      geneName: heatmapData.geneNames[geneIndex],\n+      row: geneIndex,\n+      color: pathColor\n+    };\n+    profileContent.append('path')\n+      .attr('d', line(heatmapData.values[geneIndex]))\n+      .attr('stroke', pathColor)\n+      .attr('fill', 'none')\n+      .on('mouseover', function(value) {\n+        this.data.profiles[i].container_= d3.event.target;\n+        this.signal('pathHover', this.data.profiles[i]);\n+      }.bind(this))\n+      .on('mouseout', function(value) {\n+        this.data.profiles[i].container_= d3.event.target;\n+        this.signal('pathUnhover', this.data.profiles[i]);\n+      }.bind(this))\n+      .on('click', function(value, i) {\n+        this.data.profiles[i].container_= d3.event.target;\n+        this.signal('pathClick', this.data.profiles[i]);\n+      }.bind(this));\n+  }, this);\n };\n \n /**\n- * Computes the horizontal and vertical label sizes for the heatmap.\n- * The results are stored into:\n- *     this.geneLabelWidth,\n- *     this.conditionLabelHeight\n+ * Adds the expression profiles for the selected genes as line charts.\n  * @private\n  */\n-genotet.ExpressionRenderer.prototype.getHeatmapLabelSizes_ = function() {\n-  // TODO(liana): Computes the horizontal/vertical text margin allocated for\n-  // the heatmap labels.\n-  if (!this.data.options.showGeneLabels) {\n-    this.geneLabelWidth_ = 0;\n-  } else {\n-    // To implement... replace dummy value.\n-    this.geneLabelWidth_ = 30;\n-  }\n-  if (!this.data.options.showConditionLabels) {\n-    this.conditionLabelHeight_ = 0;\n-  } else {\n-    // To implement... replace dummy value.\n-    this.conditionLabelHeight_ = 50;\n-  }\n+genotet.ExpressionRenderer.prototype.addGeneProfile_ = function(geneIndex) {\n+  var path = this.path_ = {\n+    row: geneIndex\n+  };\n+  this.data.profiles.push(path);\n+  this.drawGeneProfiles_();\n };\n \n-/** @inheritDoc */\n-genotet.ExpressionRenderer.prototype.resize = function() {\n-  this.base.resize.call(this);\n-  this.render();\n+/**\n+ * Adds the expression profiles for the selected genes as line charts.\n+ * @private\n+ */\n+genotet.ExpressionRenderer.prototype.removeGeneProfile_ = function(geneIndex) {\n+  var index = -1;\n+  this.data.profiles.forEach(function(path, i) {\n+    index = (path.row == geneIndex ? i : -1);\n+  }, this);\n+  //var index = this.data.profiles.indexOf(geneIndex);\n+  this.data.profiles.splice(index, 1);\n+  this.drawGeneProfiles_();\n };\n \n-/*\n-LayoutHeatmap.prototype.prepareLine = function() {\n-  this.lines = this.parentView.viewdata.lineData;\n-  this.maxval = this.tfaMaxval = 0;\n-  this.minval = this.tfaMinval = 1E10;\n-  for (var i = 0; i < this.lines.length; i++) {\n-    this.maxval = Math.max(Math.max.apply(null, this.lines[i].values), this.maxval);\n-    this.minval = Math.min(Math.min.apply(null, this.lines[i].values), this.minval);\n-    for (var j = 0; j < this.lines[i].tfaValues.length; j++) {\n-      this.tfaMaxval = Math.max(this.tfaMaxval, this.lines[i].tfaValues[j].value);\n-      this.tfaMinval = Math.min(this.tfaMinval, this.lines[i].tfaValues[j].value);\n-    }\n-    this.lines[i].color = this.lineColors[i];\n+/**\n+ * Highlights the hover cell for the heatmap.\n+ * @private\n+ */\n+genotet.ExpressionRenderer.prototype.highlightHoverCell_ = function(cell, highlight_) {\n+  var cellSelection = d3.select(cell.container_);\n+  if (highlight_) {\n+    cellSelection.style('stroke', 'white');\n+    this.svgGeneLabels_.selectAll('text').classed('text-highlight', function(d, i) {\n+      return cell.row == i;\n+    });\n+    this.svgConditionLabels_.selectAll('text').classed('text-highlight', function(d, i) {\n+      return cell.column == i;\n+    });\n   }\n-  var valspan = this.maxval - this.minval, tfavalspan = this.tfaMaxval - this.tfaMinval;\n-  this.maxval += valspan * 0.1; this.minval -= valspan * 0.1;\n-  this.tfaMaxval += tfavalspan * 0.1; this.tfaMinval -= tfavalspan * 0.1;\n-  this.maxvalAll = this.maxval; this.minvalAll = this.minval;\n-  this.tfaMaxvalAll = this.tfaMaxval; this.tfaMinvalAll = this.tfaMinval;\n-};\n-\n-\n-LayoutHeatmap.prototype.mouseDownLegend = function(d) {\n-  if (d3.event.button == 2) {  // right click\n-    var data = this.parentView.viewdata.lineData;\n-    for (var i = 0; i < data.length; i++) {\n-      if (data[i].name == d.name) {\n-        data.splice(i, 1);\n-        this.updateLine();\n-        return;\n-      }\n-    }\n+  else {\n+    cellSelection.style('stroke', function() {\n+      return cell.colorscaleValue;\n+    });\n+    this.svgGeneLabels_.selectAll('text').classed('text-highlight', false);\n+    this.svgConditionLabels_.selectAll('text').classed('text-highlight', false);\n   }\n };\n \n-LayoutHeatmap.prototype.unhighlightCond = function(d) {\n-  $('#'+ this.htmlid + ' #condline').attr('visibility', 'hidden');\n-  $('#'+ this.htmlid + ' #condtext').attr('visibility', 'hidden');\n-  $('#'+ this.htmlid + ' #tfacondtext').attr('visibility', 'hidden');\n-  this.svg.selectAll('#conddot'+ d.lineid + '_'+ d.index).attr('class', 'conddot');\n-  this.svg.selectAll('#tfaconddot'+ d.lineid + '_'+ d.index).attr('class', 'conddot');\n-};\n-\n-LayoutHeatmap.prototype.highlightCond = function(d, type) {\n-  //if(this.parentView.viewdata.heatmapData==null) return;  // prevent racing\n-  this.unhighlightCond(d);\n-  var layout = this;\n-  var n = this.parentView.viewdata.heatmapData.numcols;\n-  var actualWidth = this.labelrows ? this.lineWidth - this.heatmapLeft : this.lineWidth;\n-  var offsetLeft = this.labelrows ? this.heatmapLeft : 0;\n-  this.svg.selectAll('#conddot'+ d.lineid + '_'+ d.index)\n-    .attr('class', 'conddot_hl');\n-  this.svg.selectAll('#condline').data([{}])\n-    .attr('visibility', 'visible')\n-    .attr('id', 'condline')\n-    .attr('class', 'condline')\n-    .attr('x1', offsetLeft + d.index / n * actualWidth).attr('x2', offsetLeft + d.index / n * actualWidth)\n-    .attr('y1', 0).attr('y2', layout.lineHeight + (this.showTFA ? this.tfaHeight : 0));\n-\n-  var condtext = this.data.heatmapData.colnames[d.index] + ' '+ d.value.toFixed(2);\n-  var condx = offsetLeft + d.index / n * actualWidth + 5;\n-  if (condx + condtext.length * this.legendFontSize >= this.lineWidth) {\n-    condx -= 10;\n-    this.svg.selectAll('#condtext').style('text-anchor', 'end');\n-    this.svg.selectAll('#tfacondtext').style('text-anchor', 'end');\n-  }else {\n-    this.svg.selectAll('#condtext').style('text-anchor', 'start');\n-    this.svg.selectAll('#tfacondtext').style('text-anchor', 'start');\n+/**\n+ * Highlights the hover path for the gene profile.\n+ * @private\n+ */\n+genotet.ExpressionRenderer.prototype.highlightHoverPath_ = function(path, highlight_) {\n+  var pathSelection = d3.select(path.container_);\n+  if (highlight_) {\n+    pathSelection\n+      .style('stroke', 'orange')","path":"components/expression/expression-renderer.js","position":591,"original_position":591,"commit_id":"28452cfcb35381e5e91368831f7728708fb6a8d2","original_commit_id":"28452cfcb35381e5e91368831f7728708fb6a8d2","user":{"login":"yubowenok","id":1314429,"avatar_url":"https://avatars.githubusercontent.com/u/1314429?v=3","gravatar_id":"","url":"https://api.github.com/users/yubowenok","html_url":"https://github.com/yubowenok","followers_url":"https://api.github.com/users/yubowenok/followers","following_url":"https://api.github.com/users/yubowenok/following{/other_user}","gists_url":"https://api.github.com/users/yubowenok/gists{/gist_id}","starred_url":"https://api.github.com/users/yubowenok/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yubowenok/subscriptions","organizations_url":"https://api.github.com/users/yubowenok/orgs","repos_url":"https://api.github.com/users/yubowenok/repos","events_url":"https://api.github.com/users/yubowenok/events{/privacy}","received_events_url":"https://api.github.com/users/yubowenok/received_events","type":"User","site_admin":false},"body":"Please move these constant settings to css.","created_at":"2015-12-01T07:21:54Z","updated_at":"2015-12-01T07:21:54Z","html_url":"https://github.com/ViDA-NYU/genotet/pull/22#discussion_r46246660","pull_request_url":"https://api.github.com/repos/ViDA-NYU/genotet/pulls/22","_links":{"self":{"href":"https://api.github.com/repos/ViDA-NYU/genotet/pulls/comments/46246660"},"html":{"href":"https://github.com/ViDA-NYU/genotet/pull/22#discussion_r46246660"},"pull_request":{"href":"https://api.github.com/repos/ViDA-NYU/genotet/pulls/22"}}},"pull_request":{"url":"https://api.github.com/repos/ViDA-NYU/genotet/pulls/22","id":50475659,"html_url":"https://github.com/ViDA-NYU/genotet/pull/22","diff_url":"https://github.com/ViDA-NYU/genotet/pull/22.diff","patch_url":"https://github.com/ViDA-NYU/genotet/pull/22.patch","issue_url":"https://api.github.com/repos/ViDA-NYU/genotet/issues/22","number":22,"state":"open","locked":false,"title":"Rendered expression matrix as static heatmap and gene labels.","user":{"login":"Shauro","id":9913788,"avatar_url":"https://avatars.githubusercontent.com/u/9913788?v=3","gravatar_id":"","url":"https://api.github.com/users/Shauro","html_url":"https://github.com/Shauro","followers_url":"https://api.github.com/users/Shauro/followers","following_url":"https://api.github.com/users/Shauro/following{/other_user}","gists_url":"https://api.github.com/users/Shauro/gists{/gist_id}","starred_url":"https://api.github.com/users/Shauro/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Shauro/subscriptions","organizations_url":"https://api.github.com/users/Shauro/orgs","repos_url":"https://api.github.com/users/Shauro/repos","events_url":"https://api.github.com/users/Shauro/events{/privacy}","received_events_url":"https://api.github.com/users/Shauro/received_events","type":"User","site_admin":false},"body":"I rendered expression matrix as static heatmap and gene labels. I didn't finish the condition labels and and computing the horizontal/vertical text margin allocated for the heatmap labels because the interactive part and zooming part is not rendered yet. I am not very clear about the position detail of the expression view (including the zooming setting). Besides, I think the color scale need to be revised because it is not very easy to read now.","created_at":"2015-11-12T06:17:02Z","updated_at":"2015-12-01T07:21:54Z","closed_at":null,"merged_at":null,"merge_commit_sha":"ec5110859f20ea974e88205da821944664e781b1","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/ViDA-NYU/genotet/pulls/22/commits","review_comments_url":"https://api.github.com/repos/ViDA-NYU/genotet/pulls/22/comments","review_comment_url":"https://api.github.com/repos/ViDA-NYU/genotet/pulls/comments{/number}","comments_url":"https://api.github.com/repos/ViDA-NYU/genotet/issues/22/comments","statuses_url":"https://api.github.com/repos/ViDA-NYU/genotet/statuses/28452cfcb35381e5e91368831f7728708fb6a8d2","head":{"label":"ViDA-NYU:liana/refactor","ref":"liana/refactor","sha":"28452cfcb35381e5e91368831f7728708fb6a8d2","user":{"login":"ViDA-NYU","id":8114708,"avatar_url":"https://avatars.githubusercontent.com/u/8114708?v=3","gravatar_id":"","url":"https://api.github.com/users/ViDA-NYU","html_url":"https://github.com/ViDA-NYU","followers_url":"https://api.github.com/users/ViDA-NYU/followers","following_url":"https://api.github.com/users/ViDA-NYU/following{/other_user}","gists_url":"https://api.github.com/users/ViDA-NYU/gists{/gist_id}","starred_url":"https://api.github.com/users/ViDA-NYU/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ViDA-NYU/subscriptions","organizations_url":"https://api.github.com/users/ViDA-NYU/orgs","repos_url":"https://api.github.com/users/ViDA-NYU/repos","events_url":"https://api.github.com/users/ViDA-NYU/events{/privacy}","received_events_url":"https://api.github.com/users/ViDA-NYU/received_events","type":"Organization","site_admin":false},"repo":{"id":24764416,"name":"genotet","full_name":"ViDA-NYU/genotet","owner":{"login":"ViDA-NYU","id":8114708,"avatar_url":"https://avatars.githubusercontent.com/u/8114708?v=3","gravatar_id":"","url":"https://api.github.com/users/ViDA-NYU","html_url":"https://github.com/ViDA-NYU","followers_url":"https://api.github.com/users/ViDA-NYU/followers","following_url":"https://api.github.com/users/ViDA-NYU/following{/other_user}","gists_url":"https://api.github.com/users/ViDA-NYU/gists{/gist_id}","starred_url":"https://api.github.com/users/ViDA-NYU/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ViDA-NYU/subscriptions","organizations_url":"https://api.github.com/users/ViDA-NYU/orgs","repos_url":"https://api.github.com/users/ViDA-NYU/repos","events_url":"https://api.github.com/users/ViDA-NYU/events{/privacy}","received_events_url":"https://api.github.com/users/ViDA-NYU/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/ViDA-NYU/genotet","description":"Genotet: 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