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1 import sys
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2 def readTab(infile): # read in txt file
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3 with open(infile, 'r') as input_file:
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4 # read in tab-delim text
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5 output = []
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6 for input_line in input_file:
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7 input_line = input_line.strip()
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8 temp = input_line.split('\t')
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9 output.append(temp)
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10 return output
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11 def network2JSON(nodes_att_file, edge_file):
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12 nodes = readTab(nodes_att_file)
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13 edges = readTab(edge_file)
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14
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15 start = """{"nodes": ["""
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16 node_numbers = {}
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17 cnt=0
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18 for i in nodes[1:]:
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19 node_numbers[i[0]] = cnt
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20 cnt+=1
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21 start = start + '{"name":'+'"'+i[0]+'", "EV":'+i[2]+', "group":'+i[1]+"},"
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22 start = start[:-1]
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23 start = start+"""], "links": ["""
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24 for i in edges:
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25 start = start + """{"source":"""+str(node_numbers[i[0]])+""","target":"""+str(node_numbers[i[1]])+""","value":1},"""
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26 start = start[:-1]
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27 start = start + """]}"""
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28 return start
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29 def labelCentrality(nodes_att_file):
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30 nodes = readTab(nodes_att_file)
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31 if nodes[0][2] == "eigen":
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32 return "Eigenvector Centrality"
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33 if nodes[0][2] == "closeness":
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34 return "Closeness Centrality"
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35 if nodes[0][2] == "betweenness":
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36 return "Betweenness Centrality"
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37 if nodes[0][2] == "page":
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38 return "Page Rank"
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39
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40
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41
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42 adjacency_start = """
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43 <!DOCTYPE html>
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44 <html><head>
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45 <meta charset="utf-8">
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46 <style>
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47 .background {fill: #fff;}
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48 line {stroke: #000;}
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49 text.active {fill: red;font-weight:bold;}
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50 </style>
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51 <script src="http://d3js.org/d3.v2.min.js" charset="utf-8"></script>
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52 <script src="https://cdn.rawgit.com/eligrey/Blob.js/0cef2746414269b16834878a8abc52eb9d53e6bd/Blob.js""></script>
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53 <script src="https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js"></script>
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54 </head>
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55 <aside style = "margin-top: 80px">
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56 <p>Order: <select id="order">
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57 <option value="name">Name</option>
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58 <option value="EV">""" + labelCentrality(sys.argv[1]) + """</option>
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59 <option value="group">Modularity</option>
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60 </select>
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61 <button id="generate">Save as SVG</button>
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62 </aside>
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63
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64 <script>
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65 var margin = {top: 200, right: 0, bottom: 10, left: 200},
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66 width = 720,
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67 height = 720;
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68
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69 var x = d3.scale.ordinal().rangeBands([0, width]),
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70 z = d3.scale.linear().domain([0, 4]).clamp(true),
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71 c = d3.scale.category10().domain(d3.range(10));
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72
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73 var svg = d3.select("body").append("svg")
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74 .attr("id","adjmatrix")
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75 .attr("width", width + margin.left + margin.right)
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76 .attr("height", height + margin.top + margin.bottom)
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77 //.style("margin-left", -margin.left + "px")
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78 .append("g")
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79 .attr("transform", "translate(" + margin.left + "," + margin.top + ")");"""
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80
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81
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82 ################# Create JSON formatted Network ################
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83
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84 jsondata = """\njsondata ='""" + network2JSON(sys.argv[1],sys.argv[2])+"'"
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85
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86 ################################################################
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87 adjacency_end = """;
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88 var data = JSON.parse(jsondata);
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89
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90 function plot_adjacency(data) {
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91 var matrix = [],
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92 nodes = data.nodes,
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93 n = nodes.length;
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94
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95 // Compute index per node.
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96 nodes.forEach(function(node, i) {
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97 node.index = i;
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98 node.count = 0;
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99 matrix[i] = d3.range(n).map(function(j) { return {x: j, y: i, z: 0}; });
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100 });
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101
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102 // Convert edges to matrix
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103 data.links.forEach(function(link) {
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104 matrix[link.source][link.target].z += link.value;
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105 matrix[link.target][link.source].z += link.value;
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106 matrix[link.source][link.source].z += link.value; // self loop
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107 matrix[link.target][link.target].z += link.value; // self loop
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108
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109 });
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110
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111 // order based on modularity, name and eigenvector centrality
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112 var orders = {
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113 name: d3.range(n).sort(function(a, b) { return d3.ascending(nodes[a].name, nodes[b].name); }),
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114 EV: d3.range(n).sort(function(a, b) { return nodes[b].EV - nodes[a].EV; }),
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115 group: d3.range(n).sort(function(a, b) { return nodes[b].group - nodes[a].group; })
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116 };
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117
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118 // The default sort order.
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119 x.domain(orders.name);
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120
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121 svg.append("rect")
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122 .attr("class", "background")
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123 .attr("width", width)
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124 .attr("height", height)
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125 .attr("fill-opacity",0);
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126
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127 var row = svg.selectAll(".row")
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128 .data(matrix)
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129 .enter().append("g")
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130 .attr("class", "row")
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131 .attr("transform", function(d, i) { return "translate(0," + x(i) + ")"; })
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132 .each(row);
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133
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134 row.append("line")
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135 .attr("x2", width)
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136 .attr("stroke","black");
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137
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138 row.append("text")
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139 .attr("x", -6)
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140 .attr("y", x.rangeBand() / 2)
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141 .attr("dy", ".32em")
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142 .attr("text-anchor", "end")
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143 .attr("font-size", 850 * (1/nodes.length))
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144 .text(function(d, i) { return nodes[i].name; });
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145
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146 var column = svg.selectAll(".column")
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147 .data(matrix)
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148 .enter().append("g")
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149 .attr("class", "column")
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150 .attr("transform", function(d, i) { return "translate(" + x(i) + ")rotate(-90)"; });
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151
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152 column.append("line")
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153 .attr("x1", -width)
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154 .attr("stroke","black");
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155
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156 column.append("text")
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157 .attr("x", 6)
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158 .attr("y", x.rangeBand() / 2)
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159 .attr("dy", ".32em")
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160 .attr("text-anchor", "start")
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161 .style("font-style","15px")
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162 .attr("font-size", 850 * (1/nodes.length))
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163 .text(function(d, i) { return nodes[i].name; });
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164
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165 function row(row) {
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166 var cell = d3.select(this).selectAll(".cell")
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167 .data(row.filter(function(d) { return d.z; }))
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168 .enter().append("rect")
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169 .attr("class", "cell")
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170 .attr("x", function(d) { return x(d.x); })
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171 .attr("width", x.rangeBand())
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172 .attr("height", x.rangeBand())
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173 .style("fill-opacity", function(d) { return 0.4 * d.z; })
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174 .style("fill", function(d) { return nodes[d.x].group == nodes[d.y].group ? c(nodes[d.x].group) : null; })
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175 .on("mouseover", mouseover)
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176 .on("mouseout", mouseout);
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177 }
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178
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179 function mouseover(p) {
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180 d3.selectAll(".row text").classed("active", function(d, i) { return i == p.y; });
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181 d3.selectAll(".column text").classed("active", function(d, i) { return i == p.x; });
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182 }
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183
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184 function mouseout() {
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185 d3.selectAll("text").classed("active", false);
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186 }
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187
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188 d3.select("#order").on("change", function() {
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189 clearTimeout(timeout);
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190 order(this.value);
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191 });
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192
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193
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194 function order(value) {
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195 x.domain(orders[value]);
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196
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197 var t = svg.transition().duration(2500);
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198
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199 t.selectAll(".row")
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200 .delay(function(d, i) { return x(i) * 4; })
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201 .attr("transform", function(d, i) { return "translate(0," + x(i) + ")"; })
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202 .selectAll(".cell")
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203 .delay(function(d) { return x(d.x) * 4; })
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204 .attr("x", function(d) { return x(d.x); });
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205
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206 t.selectAll(".column")
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207 .delay(function(d, i) { return x(i) * 4; })
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208 .attr("transform", function(d, i) { return "translate(" + x(i) + ")rotate(-90)"; });
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209 }
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210
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211 var timeout = setTimeout(function() {
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212 order("group");
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213 d3.select("#order").property("selectedIndex", 2).node().focus();
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214 }, 5000);
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215
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216
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217 };
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218 plot_adjacency(data);
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219 d3.select("#generate")
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220 .on("click", writeDownloadLink);
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221
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222 function writeDownloadLink(){ //saving entire file instead of just SVG element
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223 try {
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224 var isFileSaverSupported = !!new Blob();
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225 } catch (e) {
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226 alert("blob not supported");
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227 }
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228
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229 var html = document.getElementById("adjmatrix").outerHTML
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230
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231 var blob = new Blob([html], {type: "image/svg+xml"});
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232 saveAs(blob, "myProfile.svg");
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233 };
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234 </script>
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235
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236
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237 </body></html>
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238 """
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239 with open(sys.argv[3],"w") as x:
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240 x.write(adjacency_start+jsondata+adjacency_end)
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