Find Peaks

This example illustrates how to use the findPeaks API. You can download the library from https://github.com/efekarakus/d3-peaks.

The algorithm is based on "Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching" by Pan Du, Warren A. Kibbe and Simon M. Lin. The paper can be found here.

forked from efekarakus's block: Find Peaks

forked from Fil's block: Find Peaks

<!DOCTYPE html>
<meta charset="utf-8">
<title>Find Peaks</title>
<style>
  .axis path,
  .axis line {
    fill: none;
    stroke: black;
    shape-rendering: crispEdges;
  }
  text {
    font-family: sans-serif;
    font-size: 11px;
  }
  
  path {
    fill: none;
    stroke: black;
    stroke-width: 1.5px;
  }
  
  path.cardinal {
    stroke: crimson;
    stroke-width: 3px;
  }
  
  path.area {
    stroke: black;
    stroke-width: 0.5px;
    fill: crimson;
    fill-opacity: 0.2;
  }
  
  circle.peak {
    fill: crimson;
  }
  
</style>
<body>
<script src="//d3js.org/d3.v3.min.js" charset="utf-8"></script>
<script src="d3-peaks.js" charset="utf-8"></script>
<script>
  var width = 920,
      height = 464,
      margin = {top: 10, left: 10, bottom: 20, right: 10};
  
  var ricker = d3_peaks.ricker;
  var findPeaks = d3_peaks.findPeaks()
    .kernel(ricker)
    .gapThreshold(1)
    .minLineLength(2)
    .minSNR(1.0)
    .widths([1,2,3]);
  
    var signal = d3.range(0,200).map(function(d) {return Math.random()*20;});
    
    var svg = d3.select("body").append("svg")
      .attr("width", width + margin.left + margin.right)
      .attr("height", height + margin.top + margin.bottom);
    var g = svg.append("g")
      .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
      
    var x = d3.scale.linear()
      .domain ([0, signal.length])
      .range([20, width]);
      
    var y = d3.scale.linear()
      .domain([0, d3.max(signal)])
      .range([height, 0]);
      
    var xAxis = d3.svg.axis()
      .scale(x)
      .ticks(20);
      
    var line = d3.svg.line()
      .x(function(d, i) { return x(i); })
      .y(function(d) { return y(d); });
      
    var area = d3.svg.area()
      .x(function(d) { return x(d.x); })
      .y0(height)
      .y1(function(d) { return y(d.y); });
      
      
    g.append("g")
      .datum(signal)
      .append("path")
      .attr("d", line);
      
    g.append("g")
      .attr("class", "axis")
      .attr("transform", "translate(0," + y(0) + ")")
      .call(xAxis);

function draw(peaks,i){
          g.selectAll(".peak"+i)
      .data(peaks)
      .enter().append("circle")
        .attr("cx", function(peak) { return x(peak.index); })
        .attr("cy", function(peak) { return y(signal[peak.index]); })
        .attr("r", 4)
        .attr("class", "peak"+i);

line.interpolate("cardinal")
      .x(function(d) { return x(d.index); })
      .y(function(d) { return y(signal[d.index]); });
      
    peaks.sort(function(a, b) { return a.index - b.index; });
    g.append("g")
      .datum(peaks)
      .append("path")
        .attr("d", line)
        .attr("class", "cardinal");
    }

draw(findPeaks(signal),1)
    draw(findPeaks(signal.map(function(d){return -d})),2)

https://d3js.org/d3.v3.min.js