Mercurial > repos > bornea > plot_adjacency

changeset 1:65551439a6bb draft default tip

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Uploaded
author bornea
date Wed, 18 Oct 2017 15:29:22 -0400
parents 8adf6ccd1077
children
files plot_adjacency.py
diffstat 1 files changed, 240 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_adjacency.py	Wed Oct 18 15:29:22 2017 -0400
@@ -0,0 +1,240 @@
+import sys
+def readTab(infile): # read in txt file
+    with open(infile, 'r') as input_file:
+    # read in tab-delim text
+        output = []
+        for input_line in input_file:
+            input_line = input_line.strip()
+            temp = input_line.split('\t')
+            output.append(temp)
+    return output
+def network2JSON(nodes_att_file, edge_file):
+	nodes = readTab(nodes_att_file)
+	edges = readTab(edge_file)
+
+	start = """{"nodes":  ["""
+  	node_numbers = {}
+  	cnt=0
+  	for i in nodes[1:]:
+  		node_numbers[i[0]] = cnt
+  		cnt+=1
+  		start = start + '{"name":'+'"'+i[0]+'", "EV":'+i[2]+', "group":'+i[1]+"},"
+  	start = start[:-1]
+  	start = start+"""], "links":  ["""
+  	for i in edges:
+  		start = start + """{"source":"""+str(node_numbers[i[0]])+""","target":"""+str(node_numbers[i[1]])+""","value":1},"""
+  	start = start[:-1]
+  	start = start + """]}"""
+  	return start
+def labelCentrality(nodes_att_file):
+	nodes = readTab(nodes_att_file)
+	if nodes[0][2] == "eigen":
+		return "Eigenvector Centrality"
+	if nodes[0][2] == "closeness":
+		return "Closeness Centrality"
+	if nodes[0][2] == "betweenness":
+		return "Betweenness Centrality"
+	if nodes[0][2] == "page":
+		return "Page Rank"
+
+
+
+adjacency_start = """
+<!DOCTYPE html>
+<html><head>
+<meta charset="utf-8">
+<style>
+.background {fill: #fff;}
+line {stroke: #000;}
+text.active {fill: red;font-weight:bold;}
+</style>
+<script src="http://d3js.org/d3.v2.min.js" charset="utf-8"></script>
+<script src="https://cdn.rawgit.com/eligrey/Blob.js/0cef2746414269b16834878a8abc52eb9d53e6bd/Blob.js""></script>
+<script src="https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js"></script>
+</head>
+<aside style = "margin-top: 80px">
+<p>Order: <select id="order">
+  <option value="name">Name</option>
+  <option value="EV">""" + labelCentrality(sys.argv[1]) + """</option>
+  <option value="group">Modularity</option>
+</select>
+<button id="generate">Save as SVG</button>
+</aside>
+
+<script>
+var margin = {top: 200, right: 0, bottom: 10, left: 200},
+    width = 720,
+    height = 720;
+
+var x = d3.scale.ordinal().rangeBands([0, width]),
+    z = d3.scale.linear().domain([0, 4]).clamp(true),
+    c = d3.scale.category10().domain(d3.range(10));
+
+var svg = d3.select("body").append("svg")
+    .attr("id","adjmatrix")
+    .attr("width", width + margin.left + margin.right)
+    .attr("height", height + margin.top + margin.bottom)
+    //.style("margin-left", -margin.left + "px")
+  .append("g")
+    .attr("transform", "translate(" + margin.left + "," + margin.top + ")");"""
+
+
+################# Create JSON formatted Network ################
+
+jsondata = """\njsondata ='""" + network2JSON(sys.argv[1],sys.argv[2])+"'"
+
+################################################################
+adjacency_end = """;
+var data = JSON.parse(jsondata);
+
+function plot_adjacency(data) {
+  var matrix = [],
+      nodes = data.nodes,
+      n = nodes.length;
+
+  // Compute index per node.
+  nodes.forEach(function(node, i) {
+    node.index = i;
+    node.count = 0;
+    matrix[i] = d3.range(n).map(function(j) { return {x: j, y: i, z: 0}; });
+  });
+
+  // Convert edges to matrix
+  data.links.forEach(function(link) {
+    matrix[link.source][link.target].z += link.value;
+    matrix[link.target][link.source].z += link.value;
+    matrix[link.source][link.source].z += link.value; // self loop
+    matrix[link.target][link.target].z += link.value; // self loop
+
+  });
+
+  // order based on modularity, name and eigenvector centrality
+  var orders = {
+    name: d3.range(n).sort(function(a, b) { return d3.ascending(nodes[a].name, nodes[b].name); }),
+    EV: d3.range(n).sort(function(a, b) { return nodes[b].EV - nodes[a].EV; }),
+    group: d3.range(n).sort(function(a, b) { return nodes[b].group - nodes[a].group; })
+  };
+
+  // The default sort order.
+  x.domain(orders.name);
+
+  svg.append("rect")
+      .attr("class", "background")
+      .attr("width", width)
+      .attr("height", height)
+      .attr("fill-opacity",0);
+
+  var row = svg.selectAll(".row")
+      .data(matrix)
+    .enter().append("g")
+      .attr("class", "row")
+      .attr("transform", function(d, i) { return "translate(0," + x(i) + ")"; })
+      .each(row);
+
+  row.append("line")
+      .attr("x2", width)
+      .attr("stroke","black");
+
+  row.append("text")
+      .attr("x", -6)
+      .attr("y", x.rangeBand() / 2)
+      .attr("dy", ".32em")
+      .attr("text-anchor", "end")
+      .attr("font-size", 850 * (1/nodes.length))
+      .text(function(d, i) { return nodes[i].name; });
+
+  var column = svg.selectAll(".column")
+      .data(matrix)
+    .enter().append("g")
+      .attr("class", "column")
+      .attr("transform", function(d, i) { return "translate(" + x(i) + ")rotate(-90)"; });
+
+  column.append("line")
+      .attr("x1", -width)
+      .attr("stroke","black");
+
+  column.append("text")
+      .attr("x", 6)
+      .attr("y", x.rangeBand() / 2)
+      .attr("dy", ".32em")
+      .attr("text-anchor", "start")
+      .style("font-style","15px")
+      .attr("font-size", 850 * (1/nodes.length))
+      .text(function(d, i) { return nodes[i].name; });
+
+  function row(row) {
+    var cell = d3.select(this).selectAll(".cell")
+        .data(row.filter(function(d) { return d.z; }))
+      .enter().append("rect")
+        .attr("class", "cell")
+        .attr("x", function(d) { return x(d.x); })
+        .attr("width", x.rangeBand())
+        .attr("height", x.rangeBand())
+        .style("fill-opacity", function(d) { return 0.4 * d.z; })
+        .style("fill", function(d) { return nodes[d.x].group == nodes[d.y].group ? c(nodes[d.x].group) : null; })
+        .on("mouseover", mouseover)
+        .on("mouseout", mouseout);
+  }
+
+  function mouseover(p) {
+    d3.selectAll(".row text").classed("active", function(d, i) { return i == p.y; });
+    d3.selectAll(".column text").classed("active", function(d, i) { return i == p.x; });
+  }
+
+  function mouseout() {
+    d3.selectAll("text").classed("active", false);
+  }
+
+  d3.select("#order").on("change", function() {
+    clearTimeout(timeout);
+    order(this.value);
+  });
+
+
+  function order(value) {
+    x.domain(orders[value]);
+
+    var t = svg.transition().duration(2500);
+
+    t.selectAll(".row")
+        .delay(function(d, i) { return x(i) * 4; })
+        .attr("transform", function(d, i) { return "translate(0," + x(i) + ")"; })
+      .selectAll(".cell")
+        .delay(function(d) { return x(d.x) * 4; })
+        .attr("x", function(d) { return x(d.x); });
+
+    t.selectAll(".column")
+        .delay(function(d, i) { return x(i) * 4; })
+        .attr("transform", function(d, i) { return "translate(" + x(i) + ")rotate(-90)"; });
+  }
+
+  var timeout = setTimeout(function() {
+    order("group");
+    d3.select("#order").property("selectedIndex", 2).node().focus();
+  }, 5000);
+
+
+};
+plot_adjacency(data);
+d3.select("#generate")
+    .on("click", writeDownloadLink);
+
+function writeDownloadLink(){ //saving entire file instead of just SVG element
+    try {
+        var isFileSaverSupported = !!new Blob();
+    } catch (e) {
+        alert("blob not supported");
+    }
+
+    var html = document.getElementById("adjmatrix").outerHTML
+
+    var blob = new Blob([html], {type: "image/svg+xml"});
+    saveAs(blob, "myProfile.svg");
+};
+</script>
+
+
+</body></html>
+"""
+with open(sys.argv[3],"w") as x:
+	x.write(adjacency_start+jsondata+adjacency_end)