Mercurial > repos > bornea > plot_force

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 + '{"id":'+'"'+i[0]+'", "size":'+str(float(i[2])*1)+', "score":'+i[1]+',"type":"circle"},'
  	start = start[:-1]
  	start = start+"""], "links":  ["""
  	for i in edges:
  			start = start + """{"source":"""+str(node_numbers[i[0]])+""","target":"""+str(node_numbers[i[1]])+"""},"""
  	start = start[:-1]
  	start = start + """]}"""
  	return start


output = """<!DOCTYPE html>
<meta charset="utf-8">
<style>
body {
  overflow:hidden;
   margin:0;
}

text {
  font-family: sans-serif;
  pointer-events: none;
}

</style>
<body>
<script src="http://d3js.org/d3.v3.min.js"></script>
<script>
jsondata='"""

output = output + network2JSON(sys.argv[1],sys.argv[2]) + "'\n"

output = output + """var w = window.innerWidth;
var h = window.innerHeight;

var keyc = true, keys = true, keyt = true, keyr = true, keyx = true, keyd = true, keyl = true, keym = true, keyh = true, key1 = true, key2 = true, key3 = true, key0 = true

var focus_node = null, highlight_node = null;

var text_center = false;
var outline = false;

var min_score = 0;
var max_score = 1;

var color = d3.scale.category20()
  .range(["green", "orange", "red","black","steelblue","purple","gray","blue","yellow","lime"]);

var highlight_color = "red";
var highlight_trans = 0.1;

var size = d3.scale.pow().exponent(1)
  .domain([1,100])
  .range([8,24]);

var force = d3.layout.force()
  .linkDistance(60)
  .charge(-500)
  .size([w,h]);

var default_node_color = "#000";
//var default_node_color = "rgb(3,190,100)";
var default_link_color = "#888";
var nominal_base_node_size = 8;
var nominal_text_size = 10;
var max_text_size = 24;
var nominal_stroke = 1.5;
var max_stroke = 4.5;
var max_base_node_size = 36;
var min_zoom = 0.1;
var max_zoom = 7;
var svg = d3.select("body").append("svg");
var zoom = d3.behavior.zoom().scaleExtent([min_zoom,max_zoom])
var g = svg.append("g");
svg.style("cursor","move");

var data = JSON.parse(jsondata);
function plot_graph(graph) {

var linkedByIndex = {};
    graph.links.forEach(function(d) {
	linkedByIndex[d.source + "," + d.target] = true;
    });

	function isConnected(a, b) {
        return linkedByIndex[a.index + "," + b.index] || linkedByIndex[b.index + "," + a.index] || a.index == b.index;
    }

	function hasConnections(a) {
		for (var property in linkedByIndex) {
				s = property.split(",");
				if ((s[0] == a.index || s[1] == a.index) && linkedByIndex[property]) 					return true;
		}
	return false;
	}

  force
    .nodes(graph.nodes)
    .links(graph.links)
    .start();

  var link = g.selectAll(".link")
    .data(graph.links)
    .enter().append("line")
    .attr("class", "link")
	.style("stroke-width",nominal_stroke)
	.style("stroke", function(d) {
	if (isNumber(d.score) && d.score>=0) return color(d.score);
	else return default_link_color; })


  var node = g.selectAll(".node")
    .data(graph.nodes)
    .enter().append("g")
    .attr("class", "node")

    .call(force.drag)


	node.on("dblclick.zoom", function(d) { d3.event.stopPropagation();
	var dcx = (window.innerWidth/2-d.x*zoom.scale());
	var dcy = (window.innerHeight/2-d.y*zoom.scale());
	zoom.translate([dcx,dcy]);
	 g.attr("transform", "translate("+ dcx + "," + dcy  + ")scale(" + zoom.scale() + ")");


	});


	var tocolor = "fill";
	var towhite = "stroke";
	if (outline) {
		tocolor = "stroke"
		towhite = "fill"
	}


  var circle = node.append("path")


      .attr("d", d3.svg.symbol()
        .size(function(d) { return Math.PI*Math.pow(size(d.size)||nominal_base_node_size,2); })
        .type(function(d) { return d.type; }))

	.style(tocolor, function(d) {
	if (isNumber(d.score) && d.score>=0) return color(d.score);
	else return default_node_color; })
    //.attr("r", function(d) { return size(d.size)||nominal_base_node_size; })
	.style("stroke-width", nominal_stroke)
	.style(towhite, "white");


  var text = g.selectAll(".text")
    .data(graph.nodes)
    .enter().append("text")
    .attr("dy", ".35em")
	.style("font-size", nominal_text_size + "px")

	if (text_center)
	 text.text(function(d) { return d.id; })
	.style("text-anchor", "middle");
	else
	text.attr("dx", function(d) {return (size(d.size)||nominal_base_node_size);})
    .text(function(d) { return '\u2002'+d.id; });

	node.on("mouseover", function(d) {
	set_highlight(d);
	})
  .on("mousedown", function(d) { d3.event.stopPropagation();
  	focus_node = d;
	set_focus(d)
	if (highlight_node === null) set_highlight(d)

}	).on("mouseout", function(d) {
		exit_highlight();

}	);

		d3.select(window).on("mouseup",
		function() {
		if (focus_node!==null)
		{
			focus_node = null;
			if (highlight_trans<1)
			{

		circle.style("opacity", 1);
	  text.style("opacity", 1);
	  link.style("opacity", 1);
	}
		}

	if (highlight_node === null) exit_highlight();
		});

function exit_highlight()
{
		highlight_node = null;
	if (focus_node===null)
	{
		svg.style("cursor","move");
		if (highlight_color!="white")
	{
  	  circle.style(towhite, "white");
	  text.style("font-weight", "normal");
	  link.style("stroke", function(o) {return (isNumber(o.score) && o.score>=0)?color(o.score):default_link_color});
 }

	}
}

function set_focus(d)
{
if (highlight_trans<1)  {
    circle.style("opacity", function(o) {
                return isConnected(d, o) ? 1 : highlight_trans;
            });

			text.style("opacity", function(o) {
                return isConnected(d, o) ? 1 : highlight_trans;
            });

            link.style("opacity", function(o) {
                return o.source.index == d.index || o.target.index == d.index ? 1 : highlight_trans;
            });
	}
}


function set_highlight(d)
{
	svg.style("cursor","pointer");
	if (focus_node!==null) d = focus_node;
	highlight_node = d;

	if (highlight_color!="white")
	{
		  circle.style(towhite, function(o) {
                return isConnected(d, o) ? highlight_color : "white";});
			text.style("font-weight", function(o) {
                return isConnected(d, o) ? "bold" : "normal";});
            link.style("stroke", function(o) {
		      return o.source.index == d.index || o.target.index == d.index ? highlight_color : ((isNumber(o.score) && o.score>=0)?color(o.score):default_link_color);

            });
	}
}


  zoom.on("zoom", function() {

    var stroke = nominal_stroke;
    if (nominal_stroke*zoom.scale()>max_stroke) stroke = max_stroke/zoom.scale();
    link.style("stroke-width",stroke);
    circle.style("stroke-width",stroke);

	var base_radius = nominal_base_node_size;
    if (nominal_base_node_size*zoom.scale()>max_base_node_size) base_radius = max_base_node_size/zoom.scale();
        circle.attr("d", d3.svg.symbol()
        .size(function(d) { return Math.PI*Math.pow(size(d.size)*base_radius/nominal_base_node_size||base_radius,2); })
        .type(function(d) { return d.type; }))

	//circle.attr("r", function(d) { return (size(d.size)*base_radius/nominal_base_node_size||base_radius); })
	if (!text_center) text.attr("dx", function(d) { return (size(d.size)*base_radius/nominal_base_node_size||base_radius); });

	var text_size = nominal_text_size;
    if (nominal_text_size*zoom.scale()>max_text_size) text_size = max_text_size/zoom.scale();
    text.style("font-size",text_size + "px");

	g.attr("transform", "translate(" + d3.event.translate + ")scale(" + d3.event.scale + ")");
	});

  svg.call(zoom);

  resize();
  //window.focus();
  d3.select(window).on("resize", resize).on("keydown", keydown);

  force.on("tick", function() {

    node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
    text.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });

    link.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; });

    node.attr("cx", function(d) { return d.x; })
      .attr("cy", function(d) { return d.y; });
	});

  function resize() {
    var width = window.innerWidth, height = window.innerHeight;
	svg.attr("width", width).attr("height", height);

	force.size([force.size()[0]+(width-w)/zoom.scale(),force.size()[1]+(height-h)/zoom.scale()]).resume();
    w = width;
	h = height;
	}

	function keydown() {
	if (d3.event.keyCode==32) {  force.stop();}
	else if (d3.event.keyCode>=48 && d3.event.keyCode<=90 && !d3.event.ctrlKey && !d3.event.altKey && !d3.event.metaKey)
	{
  switch (String.fromCharCode(d3.event.keyCode)) {
    case "C": keyc = !keyc; break;
    case "S": keys = !keys; break;
	case "T": keyt = !keyt; break;
	case "R": keyr = !keyr; break;
    case "X": keyx = !keyx; break;
	case "D": keyd = !keyd; break;
	case "L": keyl = !keyl; break;
	case "M": keym = !keym; break;
	case "H": keyh = !keyh; break;
	case "1": key1 = !key1; break;
	case "2": key2 = !key2; break;
	case "3": key3 = !key3; break;
	case "0": key0 = !key0; break;
  }

  link.style("display", function(d) {
				var flag  = vis_by_type(d.source.type)&&vis_by_type(d.target.type)&&vis_by_node_score(d.source.score)&&vis_by_node_score(d.target.score)&&vis_by_link_score(d.score);
				linkedByIndex[d.source.index + "," + d.target.index] = flag;
              return flag?"inline":"none";});
  node.style("display", function(d) {
				return (key0||hasConnections(d))&&vis_by_type(d.type)&&vis_by_node_score(d.score)?"inline":"none";});
  text.style("display", function(d) {
                return (key0||hasConnections(d))&&vis_by_type(d.type)&&vis_by_node_score(d.score)?"inline":"none";});

				if (highlight_node !== null)
				{
					if ((key0||hasConnections(highlight_node))&&vis_by_type(highlight_node.type)&&vis_by_node_score(highlight_node.score)) {
					if (focus_node!==null) set_focus(focus_node);
					set_highlight(highlight_node);
					}
					else {exit_highlight();}
				}

}
}

};

function vis_by_type(type)
{
	switch (type) {
	  case "circle": return keyc;
	  case "circle": return keys;
	  case "triangle-up": return keyt;
	  case "diamond": return keyr;
	  case "cross": return keyx;
	  case "triangle-down": return keyd;
	  default: return true;
}
}
function vis_by_node_score(score)
{
	if (isNumber(score))
	{
	if (score>=0.666) return keyh;
	else if (score>=0.333) return keym;
	else if (score>=0) return keyl;
	}
	return true;
}

function vis_by_link_score(score)
{
	if (isNumber(score))
	{
	if (score>=0.666) return key3;
	else if (score>=0.333) return key2;
	else if (score>=0) return key1;
}
	return true;
}

function isNumber(n) {
  return !isNaN(parseFloat(n)) && isFinite(n);
}
plot_graph(data)

</script>"""

with open(sys.argv[3],"w") as x:
	x.write(output)
author	bornea
date	Wed, 18 Oct 2017 15:34:23 -0400
parents	4324d3f925fe
children