move axes in separated file and complet axe document

nicgirault · Mar 11, 2017 · 0dcb9e8 · 0dcb9e8
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diff --git a/demo/axes/index.html b/demo/axes/index.html
@@ -0,0 +1,18 @@
+<!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='chart1'></div>
+    <div id='chart2'></div>
+    <div id='chart3'></div>
+    <script src='./index.js'></script>
+</body>
+</html>
diff --git a/demo/axes/index.js b/demo/axes/index.js
@@ -0,0 +1,96 @@
+var main = function(error, snp250) {
+
+  snp250 = snp250
+    .filter(function (d) {
+      return d.chromosome === 'chr2'
+    })
+    .map(function (d) {
+      return {
+        block_id: d.chromosome,
+        position: (parseInt(d.start) + parseInt(d.end)) / 2,
+        value: d.value
+      }
+    })
+
+  buildCircos('#chart1', snp250, [
+    {
+      color: 'red',
+      position: 0.002
+    },
+    {
+      color: 'green',
+      position: 0.013
+    }
+  ])
+
+  buildCircos('#chart2', snp250, [
+    {
+      color: '#333333',
+      spacing: 0.001,
+      opacity: 0.3,
+    }
+  ])
+
+  buildCircos('#chart3', snp250, [
+    {
+      color: 'red',
+      opacity: 0.3,
+      spacing: 0.001,
+      end: 0.004
+    },
+    {
+      color: 'green',
+      opacity: 0.3,
+      spacing: 0.001,
+      start: 0.011
+    },
+    {
+      color: '#333333',
+      opacity: 0.3,
+      spacing: 0.002,
+      thickness: 2,
+      start: 0.004,
+      end: 0.011
+    },
+    {
+      color: '#333333',
+      opacity: 0.3,
+      spacing: 0.001,
+      thickness: 1,
+      start: 0.004,
+      end: 0.011
+    }
+  ])
+}
+
+var buildCircos = function (container, snp250, axes) {
+  var circos = new Circos({
+    container: container,
+    width: 1000,
+    height: 1000
+  })
+
+  circos
+    .layout(
+      [{id: "chr2", color: '#03a9f4', len:243199373}],
+    {
+      innerRadius: 400,
+      outerRadius: 400,
+      labels: {display: false},
+      ticks: {display: false}
+    }
+    )
+    .line('snp-250', snp250, {
+      innerRadius: 0.5,
+      outerRadius: 0.8,
+      min: 0,
+      max: 0.015,
+      color: '#222222',
+      axes: axes,
+    })
+    .render()
+}
+
+d3.queue()
+  .defer(d3.csv, '../data/snp.density.250kb.txt')
+  .await(main)
diff --git a/doc/axes-1.png b/doc/axes-1.png
diff --git a/doc/axes-2.png b/doc/axes-2.png
diff --git a/doc/axes-3.png b/doc/axes-3.png
diff --git a/readme.md b/readme.md
@@ -14,6 +14,8 @@
   - [Scatter](#scatter)
   - [Stack](#stack)
   - [Text](#text)
+- [Colors](#colors)
+- [Axes](#axes)
 
 ## Introduction
 
@@ -519,7 +521,98 @@ The default min and max values are computed according to the dataset. You can ov
 
 ## Axes
 
+To render axes on a track, you can specify an `axes` attribute in the configuration. By default, the value of this attribute is an empty array:
 
+```javascript
+{
+  axes: []
+}
+```
+
+You can add items to this array to render an axis or a group of axes. You can give axes a `color` (default: '#d3d3d3'), `thickness` (default: 1) and `opacity` (default: track opacity):
+
+```javascript
+{
+  axes: [
+    {
+      color: 'black',
+      thickness: 2, // in pixel
+      opacity: 0.3 // between 0 and 1
+    }
+  ]
+}
+```
+
+Then you have to specify where to place the axes.
+
+You can either define single axis by defining a `position` attribute with a value between the min and max value of the track:
+
+```javascript
+{
+  axes: [
+    {
+      color: 'red',
+      position: 4
+    },
+    {
+      color: 'green',
+      position: 15
+    }
+  ]
+}
+```
+
+<p align="center">
+  <img src="doc/axes-1.png" width="60%" alt="axes-1">
+  <br/>
+  <i><a href="demo/axes">source</a></i>
+</p>
+
+
+Or define a range of axes with a `spacing` attribute and optionnally a `start` and `end` attributes.
+
+<p align="center">
+  <img src="doc/axes-2.png" width="60%" alt="axes-2">
+  <br/>
+  <i><a href="demo/axes">source</a></i>
+</p>
+
+Here is an advanced example:
+
+```javascript
+{
+  axes: [
+    {
+      color: 'red',
+      spacing: 2,
+      end: 4
+    },
+    {
+      color: 'green',
+      spacing: 2,
+      start: 16
+    },
+    {
+      spacing: 2,
+      start: 4,
+      end: 16,
+      thickness: 2
+    },
+    {
+      spacing: 1,
+      start: 4,
+      end: 16,
+      thickness: 1
+    }
+  ]
+}
+```
+
+<p align="center">
+  <img src="doc/axes-3.png" width="60%" alt="axes-3">
+  <br/>
+  <i><a href="demo/axes">source</a></i>
+</p>
 
 ## Radius
 

diff --git a/src/axes.js b/src/axes.js
@@ -0,0 +1,74 @@
+import range from 'lodash/range'
+import reduce from 'lodash/reduce'
+import {arc} from 'd3-shape'
+
+const buildAxesData = (conf) => {
+  return reduce(conf.axes, (aggregator, axesGroup) => {
+    if (axesGroup.position) {
+      aggregator.push({
+        value: axesGroup.position,
+        thickness: axesGroup.thickness || 1,
+        color: axesGroup.color || '#d3d3d3',
+        opacity: axesGroup.opacity || conf.opacity
+      })
+    }
+    if (axesGroup.spacing) {
+      const builtAxes = range(
+        axesGroup.start || conf.cmin,
+        axesGroup.end || conf.cmax,
+        axesGroup.spacing
+      )
+        .map((value) => {
+          return {
+            value: value,
+            thickness: axesGroup.thickness || 1,
+            color: axesGroup.color || '#d3d3d3',
+            opacity: axesGroup.opacity || conf.opacity
+          }
+        })
+      return aggregator.concat(builtAxes)
+    }
+    return aggregator
+  }, [])
+}
+
+export const renderAxes = (parentElement, conf, layout, scale) => {
+  const axes = buildAxesData(conf)
+
+  const axis = arc()
+    .innerRadius((d) => {
+      return conf.direction === 'in'
+        ? conf.outerRadius - scale(d.value)
+        : conf.innerRadius + scale(d.value)
+    })
+    .outerRadius((d) => {
+      return conf.direction === 'in'
+        ? conf.outerRadius - scale(d.value)
+        : conf.innerRadius + scale(d.value)
+    })
+    .startAngle(0)
+    .endAngle((d) => d.length)
+
+  return parentElement
+    .selectAll('.axis')
+      .data((blockData) => {
+        const block = layout.blocks[blockData.key]
+        return axes.map((d) => {
+          return {
+            value: d.value,
+            thickness: d.thickness,
+            color: d.color,
+            opacity: d.opacity,
+            block_id: blockData.key,
+            length: block.end - block.start
+          }
+        })
+      })
+    .enter()
+    .append('path')
+      .attr('opacity', (d) => d.opacity)
+      .attr('class', 'axis')
+      .attr('d', axis)
+      .attr('stroke-width', (d) => d.thickness)
+      .attr('stroke', (d) => d.color)
+}
diff --git a/src/tracks/Line.js b/src/tracks/Line.js
@@ -90,24 +90,26 @@ export default class Line extends Track {
       }
     }
 
-    const selection = parentElement.selectAll('.line')
-      .data((d) => conf.maxGap ? splitByGap(d.values, conf.maxGap) : [d.values])
-      .enter().append('g')
-      .attr('class', 'line')
+    const selection = parentElement
+      .selectAll('.line')
+        .data((d) => conf.maxGap ? splitByGap(d.values, conf.maxGap) : [d.values])
+      .enter()
+      .append('g')
+        .attr('class', 'line')
       .append('path')
-      .datum((d) => {
-        return d.map((datum) => {
-          const height = this.scale(datum.value)
-          return assign(datum, {
-            angle: this.theta(datum.position, layout.blocks[datum.block_id])
-          }, buildRadius(height))
+        .datum((d) => {
+          return d.map((datum) => {
+            const height = this.scale(datum.value)
+            return assign(datum, {
+              angle: this.theta(datum.position, layout.blocks[datum.block_id])
+            }, buildRadius(height))
+          })
         })
-      })
-      .attr('d', generator)
-      .attr('opacity', conf.opacity)
-      .attr('stroke-width', conf.thickness)
-      .attr('stroke', conf.colorValue)
-      .attr('fill', 'none')
+        .attr('d', generator)
+        .attr('opacity', conf.opacity)
+        .attr('stroke-width', conf.thickness)
+        .attr('stroke', conf.colorValue)
+        .attr('fill', 'none')
 
     if (conf.fill) { selection.attr('fill', conf.fillColor) }