Mercurial > repos > bornea > plot_adjacency

comparison plot_adjacency.py @ 1:65551439a6bb draft default tip

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author bornea
date Wed, 18 Oct 2017 15:29:22 -0400
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0:8adf6ccd1077 1:65551439a6bb
1 import sys
2 def readTab(infile): # read in txt file
3 with open(infile, 'r') as input_file:
4 # read in tab-delim text
5 output = []
6 for input_line in input_file:
7 input_line = input_line.strip()
8 temp = input_line.split('\t')
9 output.append(temp)
10 return output
11 def network2JSON(nodes_att_file, edge_file):
12 nodes = readTab(nodes_att_file)
13 edges = readTab(edge_file)
14
15 start = """{"nodes": ["""
16 node_numbers = {}
17 cnt=0
18 for i in nodes[1:]:
19 node_numbers[i[0]] = cnt
20 cnt+=1
21 start = start + '{"name":'+'"'+i[0]+'", "EV":'+i[2]+', "group":'+i[1]+"},"
22 start = start[:-1]
23 start = start+"""], "links": ["""
24 for i in edges:
25 start = start + """{"source":"""+str(node_numbers[i[0]])+""","target":"""+str(node_numbers[i[1]])+""","value":1},"""
26 start = start[:-1]
27 start = start + """]}"""
28 return start
29 def labelCentrality(nodes_att_file):
30 nodes = readTab(nodes_att_file)
31 if nodes[0][2] == "eigen":
32 return "Eigenvector Centrality"
33 if nodes[0][2] == "closeness":
34 return "Closeness Centrality"
35 if nodes[0][2] == "betweenness":
36 return "Betweenness Centrality"
37 if nodes[0][2] == "page":
38 return "Page Rank"
39
40
41
42 adjacency_start = """
43 <!DOCTYPE html>
44 <html><head>
45 <meta charset="utf-8">
46 <style>
47 .background {fill: #fff;}
48 line {stroke: #000;}
49 text.active {fill: red;font-weight:bold;}
50 </style>
51 <script src="http://d3js.org/d3.v2.min.js" charset="utf-8"></script>
52 <script src="https://cdn.rawgit.com/eligrey/Blob.js/0cef2746414269b16834878a8abc52eb9d53e6bd/Blob.js""></script>
53 <script src="https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js"></script>
54 </head>
55 <aside style = "margin-top: 80px">
56 <p>Order: <select id="order">
57 <option value="name">Name</option>
58 <option value="EV">""" + labelCentrality(sys.argv[1]) + """</option>
59 <option value="group">Modularity</option>
60 </select>
61 <button id="generate">Save as SVG</button>
62 </aside>
63
64 <script>
65 var margin = {top: 200, right: 0, bottom: 10, left: 200},
66 width = 720,
67 height = 720;
68
69 var x = d3.scale.ordinal().rangeBands([0, width]),
70 z = d3.scale.linear().domain([0, 4]).clamp(true),
71 c = d3.scale.category10().domain(d3.range(10));
72
73 var svg = d3.select("body").append("svg")
74 .attr("id","adjmatrix")
75 .attr("width", width + margin.left + margin.right)
76 .attr("height", height + margin.top + margin.bottom)
77 //.style("margin-left", -margin.left + "px")
78 .append("g")
79 .attr("transform", "translate(" + margin.left + "," + margin.top + ")");"""
80
81
82 ################# Create JSON formatted Network ################
83
84 jsondata = """\njsondata ='""" + network2JSON(sys.argv[1],sys.argv[2])+"'"
85
86 ################################################################
87 adjacency_end = """;
88 var data = JSON.parse(jsondata);
89
90 function plot_adjacency(data) {
91 var matrix = [],
92 nodes = data.nodes,
93 n = nodes.length;
94
95 // Compute index per node.
96 nodes.forEach(function(node, i) {
97 node.index = i;
98 node.count = 0;
99 matrix[i] = d3.range(n).map(function(j) { return {x: j, y: i, z: 0}; });
100 });
101
102 // Convert edges to matrix
103 data.links.forEach(function(link) {
104 matrix[link.source][link.target].z += link.value;
105 matrix[link.target][link.source].z += link.value;
106 matrix[link.source][link.source].z += link.value; // self loop
107 matrix[link.target][link.target].z += link.value; // self loop
108
109 });
110
111 // order based on modularity, name and eigenvector centrality
112 var orders = {
113 name: d3.range(n).sort(function(a, b) { return d3.ascending(nodes[a].name, nodes[b].name); }),
114 EV: d3.range(n).sort(function(a, b) { return nodes[b].EV - nodes[a].EV; }),
115 group: d3.range(n).sort(function(a, b) { return nodes[b].group - nodes[a].group; })
116 };
117
118 // The default sort order.
119 x.domain(orders.name);
120
121 svg.append("rect")
122 .attr("class", "background")
123 .attr("width", width)
124 .attr("height", height)
125 .attr("fill-opacity",0);
126
127 var row = svg.selectAll(".row")
128 .data(matrix)
129 .enter().append("g")
130 .attr("class", "row")
131 .attr("transform", function(d, i) { return "translate(0," + x(i) + ")"; })
132 .each(row);
133
134 row.append("line")
135 .attr("x2", width)
136 .attr("stroke","black");
137
138 row.append("text")
139 .attr("x", -6)
140 .attr("y", x.rangeBand() / 2)
141 .attr("dy", ".32em")
142 .attr("text-anchor", "end")
143 .attr("font-size", 850 * (1/nodes.length))
144 .text(function(d, i) { return nodes[i].name; });
145
146 var column = svg.selectAll(".column")
147 .data(matrix)
148 .enter().append("g")
149 .attr("class", "column")
150 .attr("transform", function(d, i) { return "translate(" + x(i) + ")rotate(-90)"; });
151
152 column.append("line")
153 .attr("x1", -width)
154 .attr("stroke","black");
155
156 column.append("text")
157 .attr("x", 6)
158 .attr("y", x.rangeBand() / 2)
159 .attr("dy", ".32em")
160 .attr("text-anchor", "start")
161 .style("font-style","15px")
162 .attr("font-size", 850 * (1/nodes.length))
163 .text(function(d, i) { return nodes[i].name; });
164
165 function row(row) {
166 var cell = d3.select(this).selectAll(".cell")
167 .data(row.filter(function(d) { return d.z; }))
168 .enter().append("rect")
169 .attr("class", "cell")
170 .attr("x", function(d) { return x(d.x); })
171 .attr("width", x.rangeBand())
172 .attr("height", x.rangeBand())
173 .style("fill-opacity", function(d) { return 0.4 * d.z; })
174 .style("fill", function(d) { return nodes[d.x].group == nodes[d.y].group ? c(nodes[d.x].group) : null; })
175 .on("mouseover", mouseover)
176 .on("mouseout", mouseout);
177 }
178
179 function mouseover(p) {
180 d3.selectAll(".row text").classed("active", function(d, i) { return i == p.y; });
181 d3.selectAll(".column text").classed("active", function(d, i) { return i == p.x; });
182 }
183
184 function mouseout() {
185 d3.selectAll("text").classed("active", false);
186 }
187
188 d3.select("#order").on("change", function() {
189 clearTimeout(timeout);
190 order(this.value);
191 });
192
193
194 function order(value) {
195 x.domain(orders[value]);
196
197 var t = svg.transition().duration(2500);
198
199 t.selectAll(".row")
200 .delay(function(d, i) { return x(i) * 4; })
201 .attr("transform", function(d, i) { return "translate(0," + x(i) + ")"; })
202 .selectAll(".cell")
203 .delay(function(d) { return x(d.x) * 4; })
204 .attr("x", function(d) { return x(d.x); });
205
206 t.selectAll(".column")
207 .delay(function(d, i) { return x(i) * 4; })
208 .attr("transform", function(d, i) { return "translate(" + x(i) + ")rotate(-90)"; });
209 }
210
211 var timeout = setTimeout(function() {
212 order("group");
213 d3.select("#order").property("selectedIndex", 2).node().focus();
214 }, 5000);
215
216
217 };
218 plot_adjacency(data);
219 d3.select("#generate")
220 .on("click", writeDownloadLink);
221
222 function writeDownloadLink(){ //saving entire file instead of just SVG element
223 try {
224 var isFileSaverSupported = !!new Blob();
225 } catch (e) {
226 alert("blob not supported");
227 }
228
229 var html = document.getElementById("adjmatrix").outerHTML
230
231 var blob = new Blob([html], {type: "image/svg+xml"});
232 saveAs(blob, "myProfile.svg");
233 };
234 </script>
235
236
237 </body></html>
238 """
239 with open(sys.argv[3],"w") as x:
240 x.write(adjacency_start+jsondata+adjacency_end)