vega with existing d3 hierarchy

StackOverflow question

<!DOCTYPE html>
<html>
<head>
  
  <script src="https://unpkg.com/d3"></script>
  <script src="https://cdnjs.cloudflare.com/ajax/libs/vega/3.0.0-rc4/vega-core.min.js"></script>
  <script src="https://cdnjs.cloudflare.com/ajax/libs/vega-lite/2.0.0-beta.10/vega-lite.min.js"></script>
  
  <script src="https://cdnjs.cloudflare.com/ajax/libs/vega-embed/3.0.0-beta.19/vega-embed.min.js"></script>
</head>
<body>

var spec = {
  "$schema": "https://vega.github.io/schema/vega/v3.0.json",
  "width": 960,
  "height": 500,
  "padding": 2.5,
  "autosize": "none",

"data": [
    {
      "name": "nodes",
      "values": flare_tm.descendants().filter(d=>d.depth===1)
    },
    
    {
      "name": "leaves",
      "values": flare_tm.leaves()
    }
  ],

"scales": [
    {
      "name": "color",
      "type": "ordinal",
      "range": [
        "#3182bd", "#6baed6", "#9ecae1", "#c6dbef", "#e6550d",
        "#fd8d3c", "#fdae6b", "#fdd0a2", "#31a354", "#74c476",
        "#a1d99b", "#c7e9c0", "#756bb1", "#9e9ac8", "#bcbddc",
        "#dadaeb", "#636363", "#969696", "#bdbdbd", "#d9d9d9"
      ]
    },
    {
      "name": "size",
      "type": "ordinal",
      "domain": [0, 1, 2, 3],
      "range": [256, 28, 20, 14]
    },
    {
      "name": "opacity",
      "type": "ordinal",
      "domain": [0, 1, 2, 3],
      "range": [0.15, 0.5, 0.8, 1.0]
    }
  ],

"marks": [
    {
      "type": "rect",
      "from": {"data": "nodes"},
      "interactive": false,
      "encode": {
        "enter": {
          "fill": {"scale": "color", "field": "data.name"}
        },
        "update": {
          "x": {"field": "x0"},
          "y": {"field": "y0"},
          "x2": {"field": "x1"},
          "y2": {"field": "y1"}
        }
      }
    },
    {
      "type": "rect",
      "from": {"data": "leaves"},
      "encode": {
        "enter": {
          "stroke": {"value": "#fff"}
        },
        "update": {
          "x": {"field": "x0"},
          "y": {"field": "y0"},
          "x2": {"field": "x1"},
          "y2": {"field": "y1"},
          "fill": {"value": "transparent"}
        },
        "hover": {
          "fill": {"value": "red"}
        }
      }
    },
    {
      "type": "text",
      "from": {"data": "nodes"},
      "interactive": false,
      "encode": {
        "enter": {
          "font": {"value": "Helvetica Neue, Arial"},
          "align": {"value": "center"},
          "baseline": {"value": "middle"},
          "fill": {"value": "#000"},
          "text": {"field": "data.name"},
          "fontSize": {"scale": "size", "field": "depth"},
          "fillOpacity": {"scale": "opacity", "field": "depth"}
        },
        "update": {
          "x": {"signal": "0.5 * (datum.x0 + datum.x1)"},
          "y": {"signal": "0.5 * (datum.y0 + datum.y1)"}
        }
      }
    }
  ]
}

vega.embed('#vis', spec, {'renderer':'svg'});
  })
</script>
</body>
</html>

https://unpkg.com/d3

https://cdnjs.cloudflare.com/ajax/libs/vega/3.0.0-rc4/vega-core.min.js

https://cdnjs.cloudflare.com/ajax/libs/vega-lite/2.0.0-beta.10/vega-lite.min.js

https://cdnjs.cloudflare.com/ajax/libs/vega-embed/3.0.0-beta.19/vega-embed.min.js