Demo Stacked

<!DOCTYPE html>
<meta charset="utf-8">

<script src="https://d3js.org/d3.v4.js"></script>
<script src="https://d3js.org/d3-scale-chromatic.v1.min.js"></script>

<div id="my_dataviz"></div>

// set the dimensions and margins of the graph
var margin = {top: 10, right: 30, bottom: 20, left: 50},
    width = 460 - margin.left - margin.right,
    height = 400 - margin.top - margin.bottom;

// append the svg object to the body of the page
var svg = d3.select("#my_dataviz")
  .append("svg")
    .attr("width", width + margin.left + margin.right)
    .attr("height", height + margin.top + margin.bottom)
  .append("g")
    .attr("transform",
          "translate(" + margin.left + "," + margin.top + ")");

// Parse the Data
d3.csv("data.csv", function(data) {

// List of subgroups = header of the csv files = soil condition here
  var subgroups = data.columns.slice(1)

// List of groups = species here = value of the first column called group -> I show them on the X axis
  var groups = d3.map(data, function(d){return(d.group)}).keys()

// Add X axis
  var x = d3.scaleBand()
      .domain(groups)
      .range([0, width])
      .padding([0.2])
  svg.append("g")
    .attr("transform", "translate(0," + height + ")")
    .call(d3.axisBottom(x).tickSizeOuter(0));

// Add Y axis
  var y = d3.scaleLinear()
    .domain([0, 120])
    .range([ height, 0 ]);
  svg.append("g")
    .call(d3.axisLeft(y));

// color palette = one color per subgroup
  var color = d3.scaleOrdinal()
    .domain(subgroups)
    .range(d3.schemeSet2);

//stack the data? --> stack per subgroup
  var stackedData = d3.stack()
    .keys(subgroups)
    (data)

console.log(subgroups);
console.log(data);

// ----------------
  // Highlight a specific subgroup when hovered
  // ----------------

// What happens when user hover a bar
  var mouseover = function(d) {
    // what subgroup are we hovering?
    var subgroupName = d3.select(this.parentNode).datum().key; // This was the tricky part
    var subgroupValue = d.data[subgroupName];
    // Reduce opacity of all rect to 0.2
    d3.selectAll(".myRect").style("opacity", 0.2)
    // Highlight all rects of this subgroup with opacity 0.8. It is possible to select them since they have a specific class = their name.
    d3.selectAll("."+subgroupName)
      .style("opacity", 1)
    }

// When user do not hover anymore
  var mouseleave = function(d) {
    // Back to normal opacity: 0.8
    d3.selectAll(".myRect")
      .style("opacity",0.8)
    }

// Show the bars
  svg.append("g")
    .selectAll("g")
    // Enter in the stack data = loop key per key = group per group
    .data(stackedData)
    .enter().append("g")
      .attr("fill", function(d) { return color(d.key); })
      .attr("class", function(d){ return "myRect " + d.key }) // Add a class to each subgroup: their name
      .selectAll("rect")
      // enter a second time = loop subgroup per subgroup to add all rectangles
      .data(function(d) { return d; })
      .enter().append("rect")
        .attr("x", function(d) { return x(d.data.group); })
        .attr("y", function(d) { return y(d[1]); })
        .attr("height", function(d) { return y(d[0]) - y(d[1]); })
        .attr("width",x.bandwidth())
        .attr("stroke", "grey")
      .on("mouseover", mouseover)
      .on("mouseleave", mouseleave)

})

</script>

https://d3js.org/d3.v4.js

https://d3js.org/d3-scale-chromatic.v1.min.js