score:0

Then you need to change the color based on the group. Change this line as follow:

.attr("fill", function(d) {return color(d.group)})

Please find the working code below:

var graph = {
  'nodes': [{
      'id': 'Material_Definition',
      'group': 0
    },
    {
      'id': 'Item1',
      'group': 1
    },
    {
      'id': 'Item2',
      'group': 1
    },
    {
      'id': 'Item3',
      'group': 1
    },
    {
      'id': 'Item4',
      'group': 1
    },
    {
      'id': 'Item5',
      'group': 1
    },
    {
      'id': 'SubItem1_Item1',
      'group': 2
    },
    {
      'id': 'SubItem2_Item1',
      'group': 2
    }
  ],
  'links': [
    /* Material Definition linked to Items */
    {
      'source': 'Material_Definition',
      'target': 'Item1',
      'value': 1,
      'type': 'A'
    },
    {
      'source': 'Material_Definition',
      'target': 'Item2',
      'value': 8,
      'type': 'A'
    },
    {
      'source': 'Material_Definition',
      'target': 'Item3',
      'value': 10,
      'type': 'A'
    },
    {
      'source': 'Material_Definition',
      'target': 'Item3',
      'value': 1,
      'type': 'A'
    },
    {
      'source': 'Material_Definition',
      'target': 'Item4',
      'value': 1,
      'type': 'A'
    },
    {
      'source': 'Material_Definition',
      'target': 'Item5',
      'value': 1,
      'type': 'A'
    },

    /* Item1 is linked to SubItems */
    {
      'source': 'Item1',
      'target': 'SubItem1_Item1',
      'value': 2,
      'type': 'A'
    },
    {
      'source': 'Item1',
      'target': 'SubItem2_Item1',
      'value': 1,
      'type': 'A'
    },

    /* Interconnected Items */
    {
      'source': 'Item5',
      'target': 'Item4',
      'value': 2,
      'type': 'A'
    },
    {
      'source': 'Item2',
      'target': 'Item3',
      'value': 1,
      'type': 'A'
    },
  ]
};



var svg = d3.select("svg"),
  width = +svg.attr("width"),
  height = +svg.attr("height")

var store = Object.assign({}, graph);
var color = d3.scaleOrdinal(d3.schemeCategory10);
var zoom_handler = d3.zoom().on("zoom", zoom_actions);
var linkElements, nodeElements, textElements, grads;

// zoom_handler(svg);

var simulation = d3.forceSimulation()
  .force("link", d3.forceLink().distance(700).id(function(d) {
    return d.id;
  }))
  .force("charge", d3.forceManyBody().strength(-1000))

  .force("center", d3.forceCenter(width / 2, height / 2));

var g = svg.append("g")
  .attr("class", "everything");

svg.call(zoom_handler)
  .call(zoom_handler.transform, d3.zoomIdentity.translate(200, 150).scale(0.2));
linkElements = svg.append("g").selectAll(".link"),
  nodeElements = svg.append("g").selectAll(".nodes");
grads = svg.append("g").selectAll(".grads");
textElements = svg.append("g").selectAll(".texts");
drawGraph();


function drawGraph() {

  // empty current Graph contents
  g.html('')

  grads = svg.append("defs").selectAll("radialGradient")
    .data(graph.nodes)
    .enter()
    .append("radialGradient")
    .attr("gradientUnits", "objectBoundingBox")
    .attr("cx", 0)
    .attr("fill", function(d) {
      return color(d.group);
    })
    .attr("cy", 0)
    .attr("r", "100%")
    .attr("id", function(d, i) {
      return "grad" + i;
    });

  grads.append("stop")
    .attr("offset", "0%")
    .style("stop-color", "white");

  grads.append("stop")
    .attr("offset", "100%")
    .style("stop-color", function(d) {
      return color(d.id);
    });


  linkElements = g.append("g")
    .attr("class", "links")
    .selectAll("line")
    .data(graph.links)
    .enter().append("line")
    .style("stroke-width", 5.5)
    .style("stroke", "grey")


  nodeElements = g.append("g")
    .attr("class", "nodes")
    .selectAll("circle")
    .data(graph.nodes)
    .enter().append("circle")
    .attr("r", 60)

    .attr("stroke", "#fff")
    .attr('stroke-width', 21)
    .attr("id", function(d) {
      return d.id
    })
    .attr("fill", function(d) {
      return color(d.group)
    })
    /*      .attr('fill', function(d, i) { return 'url(#grad' + i + ')'; }) */
    .on('contextmenu', function(d) {
      d3.event.preventDefault();
      menu(d3.mouse(svg.node())[0], d3.mouse(svg.node())[1]);
    })
    .on('mouseover', selectNode)
    .on('mouseout', releaseNode)
    .call(d3.drag()
      .on("start", dragstarted)
      .on("drag", dragged)
      .on("end", dragended));

  textElements = g.append("g") // use g.append instead of svg.append to enable zoom
    .attr("class", "texts")
    .selectAll("text")
    .data(graph.nodes)
    .enter().append("text")
    .attr("text-anchor", "end")
    .text(function(node) {
      return node.id
    })
    .attr("font-size", 55)
    .attr("font-family", "sans-serif")
    .attr("fill", "black")
    .attr("style", "font-weight:bold;")
    .attr("dx", 30)
    .attr("dy", 80)

}

function ticked() {
  linkElements
    .attr("x1", function(d) {
      return d.source.x;
    })
    .attr("y1", function(d) {
      return d.source.y;
    })
    .attr("x2", function(d) {
      return d.target.x;
    })
    .attr("y2", function(d) {
      return d.target.y;
    });
  nodeElements
    .attr("cx", function(d) {
      return d.x;
    })
    .attr("cy", function(d) {
      return d.y;
    })
    .each(d => {
      d3.select('#t_' + d.id).attr('x', d.x + 10).attr('y', d.y + 3);
    });
  textElements
    .attr('x', function(d) {
      return d.x
    })
    .attr('y', function(d) {
      return d.y
    });
}

simulation
  .nodes(graph.nodes)
  .on("tick", ticked);

simulation.force("link")
  .links(graph.links);


function zoom_actions() {
  g.attr("transform", d3.event.transform)
}

function dragstarted(d) {
  if (!d3.event.active) simulation.alphaTarget(0.3).restart();
  d.fx = d.x;
  d.fy = d.y;
}

function dragged(d) {
  d.fx = d3.event.x;
  d.fy = d3.event.y;
}

function dragended(d) {
  if (!d3.event.active) simulation.alphaTarget(0);
  d.fx = null;
  d.fy = null;
}

function selectNode(selectedNode) {
  var neighbors = getNeighbors(selectedNode)

  nodeElements.transition().duration(500)
    .attr('r', function(node) {
      return getNodeRadius(node, neighbors);
    });

  nodeElements.attr('fill', function(node) {
    return getNodeColor(node, neighbors, selectedNode);
  })


  textElements.transition().duration(500).style('font-size', function(node) {
    return getTextColor(node, neighbors)
  })
}

function releaseNode() {
  nodeElements.transition().duration(500)
    .attr('r', 60);
  nodeElements.attr('fill', function(d, i) {
    return 'url(#grad' + i + ')';
  })

  linkElements.style('stroke', 'grey');
}

function getNeighbors(node) {
  return graph.links.reduce(function(neighbors, link) {
    if (link.target.id === node.id) {
      neighbors.push(link.source.id)
    } else if (link.source.id === node.id) {
      neighbors.push(link.target.id)
    }
    return neighbors
  }, [node.id])
}

function getNodeColor(node, neighbors, selectedNode) {
  // If is neighbor
  if (Array.isArray(neighbors) && neighbors.indexOf(node.id) > -1) {
    return 'url(#grad' + selectedNode.index + ')'
    // return node.level === 1 ? '#9C4A9C' : 'rgba(251, 130, 30, 1)'
  } else {
    return 'url(#grad' + node.index + ')'
  }
  //return node.level === 0 ? '#91007B' : '#D8ABD8'
}

function getNodeRadius(node, neighbors) {
  // If is neighbor
  if (neighbors.indexOf(node.id) > -1) {
    return '100'
  } else {
    return '60'
  }
}

function isNeighborLink(node, link) {
  return link.target.id === node.id || link.source.id === node.id
}

function getTextColor(node, neighbors) {
  return Array.isArray(neighbors) && neighbors.indexOf(node.id) > -1 ? '40px' : '25px'
}


var filter = document.querySelector('#filter');
filter.addEventListener('change', function(event) {
  filterData(event.target.value);
  drawGraph();
})

var resetFilter = document.querySelector('#reset');
resetFilter.addEventListener('click', function(event) {
  drawGraph();
})

function filterData(id) {
  graph = Object.assign({}, store);
  graph.nodes = [];
  graph.links = [];
  dummyStore = [id];
  store.links.forEach(function(link) {
    if (link.source.id === id) {
      graph.links.push(link);
      dummyStore.push(link.target.id);
    } else if (link.target.id === id) {
      graph.links.push(link);
      dummyStore.push(link.source.id)
    }
  });
  store.nodes.forEach(function(node) {
    if (dummyStore.includes(node.id)) {
      graph.nodes.push(node);
    }
  })
}
.links line {
  stroke: #999;
  stroke-opacity: 0.6;
}

.nodes circle {
  stroke: #000;
  stroke-width: 1.5px;
}

text {
  font-size: 10px;
}
<script src="https://d3js.org/d3.v4.min.js"></script>
Filter: <input type="text" name="filter" id="filter" />
<button id='reset'>Reset Filter</button>
<svg width="798" height="400"></svg>


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