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See merge request bax9187/projekt-cis-biochemie-2021-22!4
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# Projekt CiS-Projekt 2021/22
Citation network made with **d3.js**
## Usage
### Input
Json file **json\_text.json** in directory
```json
{
"nodes": [
{
"name": <title: string>,
"author": [<author1: string>, <author2: string>, ...],
"year": <date: tring>,
"journal": <journal: string>,
"doi": <doi: string>,
"group": <"input"/"height"/"depth">,
"citations": <citation: int>
}, ...
],
"links": [
{
"source": <doi: string>,
"target": <doi: string>
}, ...
]
}
```
### Display the Citation Network
Starting a python web server:
```sh
cd <path to file> &&python3 -m http.server <port>
```
Access to the server:
[http://0.0.0.0/:\<port\>](http://0.0.0.0/:<port>)
## Files in Directory
- **index.html**: webpage
- **cn.js**: javascript code for force-directed graph, text elements and legend
- **json_text.json**: example data
## Authors
- Katja Ehlers
- Merle Stahl
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/**
* creates a new zoom behavior
*/
var zoom = d3.zoom().on("zoom", handle_zoom);
/**
* creates svg object and associated attributes
* applies the zoom behavior to svg
*/
var svg = d3.select("svg.graph")
.call(zoom),
width = svg.attr("width"),
height = svg.attr("height"),
perc;
/**
* scale functions that return y coordinate/color of node depending on group
*/
var color = d3.scaleOrdinal()
.domain(["height", "input", "depth"])
.range([' #01d7c0', ' #8b90fe ', ' #a15eb2 ']),
y_scale = d3.scaleOrdinal()
.domain(["height", "input", "depth"])
.range([0, 200, 400]),
to_remove;
/**
* creates node object and (default) radius
*/
var node,
r = 10;
/**
* creates link object
*/
var link;
/**
* creates a background with a click functionality
*/
var rect = svg.append("rect")
.attr("x", 0)
.attr("y", 0)
.attr("height", height)
.attr("width", width)
.style("fill", 'white')
.on('click', click_rect);
/**
* creates svg object (legend) and associated attributes
*/
var svg_legend = d3.select("svg.legendsvg"),
legend_position = [65,95,125],
arrow_legend_position = [0,25],
arrow_group_names = ["citation","self-citation"],
group_names = ["cited by","input","reference"],
line_type = d3.scaleOrdinal()
.domain(["line","dotted"])
.range([("8,0"),("8,8")]),
text_info = '',
text_abstract = '';
var legend = svg_legend.selectAll(".legend")
.data(legend_position)
.enter()
.append("g")
.attr("class","legend")
.attr("transform", function(d,i) {return "translate(0," + d + ")"; });
legend.append("text")
.attr("x", 80)
.attr("y", 0)
.attr("dy", ".35em")
.style("text-anchor", "start")
.text(function(d,i) {return group_names[i]});
legend.append("circle")
.attr("r", r)
.attr("cx",30-r)
.style("fill", color);
var legend_arrow = svg_legend.selectAll(".legendarr")
.data(arrow_legend_position)
.enter()
.append("g")
.attr("class","legendarr")
.attr("transform", function(d) { return "translate(0," + d + ")"; });
legend_arrow.append("line")
.attr("x1", 10)
.attr("x2", 50)
.attr("y1", 10)
.attr("y2", 10)
.style("stroke-dasharray",line_type)
.style("stroke", '#999')
.style("stroke-width", "1px")
.style('pointer-events', 'none')
.attr('marker-end',update_marker('#999',this));
legend_arrow.append("text")
.attr("x", 80)
.attr("y", 10)
.attr("dy", ".35em")
.style("text-anchor", "start")
.text(function(d,i){return arrow_group_names[i]});
/**
* creates a new simulation
* updates the positions of the links and nodes when the
state of the layout has changed (simulation has advanced by a tick)
*/
var simulation = d3.forceSimulation()
.force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(50).strength(function(d) {
if (d.group == "input") {return 0;}
else {return 5;}
}))
.force("collide", d3.forceCollide(function(d) {
if (d.group == "input") {return 100;}
else {return 65;}
}).strength(0.5))
.force("charge", d3.forceManyBody().strength(0.001))
.force("center", d3.forceCenter(width/2, height/2+20))
.force("yscale", d3.forceY().strength(function(d) {
if (d.group == "input") {return 1000;}
else {return 50;}
}).y(function(d) {return y_scale(d.group)}))
.alpha(0.005)
.on("end", zoom_to);
/**
* creates group element
*/
var g = svg.append("g")
.attr("class", "everything")
/**
* loads JSON data and calls the update function
*/
d3.json("json_text.json").then(function(graph) {
update(graph.links, graph.nodes);
})
/**
* calls update functions for links and nodes
* adds the nodes, links and tick functionality to the simulation
* @param {object} nodes - nodes
* @param {object} links - links
*/
function update(links, nodes) {
update_links(links);
update_nodes(nodes);
simulation
.nodes(nodes)
.on("tick", handle_tick);
simulation.force("link")
.links(links);
link.attr('marker-end', function(d) {return update_marker("#999", d.target);})
.style("stroke-dasharray",function(d){return self_citation(d.source,d.target)? ("8,8"): ("1,0")});
}
/**
* initializes and shows links
* @param {object} links - links
*/
function update_links(links) {
link = g.append("g")
.selectAll(".link")
.data(links)
.enter()
.append("line")
.style("stroke-width", "1px")
.style("stroke", "#999")
.attr("class", "link");
}
/**
* initializes and shows nodes with circles, texts and a click functionality
* creates a new drag behavior and applies it to the circles
* @param {object} nodes - nodes
*/
function update_nodes(nodes) {
node = g.selectAll(".node")
.data(nodes)
.enter()
.append("g")
.attr("class", "node")
.call(d3.drag()
.on("start", start_drag)
.on("drag", dragged)
);
node.append("circle")
.attr("class", "circle")
.attr("r", function(d) {return 1.5*r+d.citations*0.05})
.style("fill", function(d){ return color(d.group)})
.on('click', click_node);
node.append("text")
.attr("class", "text")
.style("font-size", "15px")
.style('pointer-events', 'auto')
.text(function (d) {const first_author=d.author[0].split(" ")
return first_author[first_author.length-1];})
.on('click', click_node);
}
/**
* creates arrowhead and returns its url
* @param {string} color - color of arrowhead
* @param {string} target - target node
*/
function update_marker(color, target) {
var radius = 1.5*r+target.citations*0.05;
svg.append('defs').append('marker')
.attr('id',color.replace("#", "")+radius)
.attr('viewBox','-0 -5 10 10')
.attr('refX',radius+9.5)
.attr('refY',0)
.attr('orient','auto')
.attr('markerWidth',10)
.attr('markerHeight',15)
.attr('xoverflow','visible')
.append('svg:path')
.attr('d', 'M 0,-5 L 10 ,0 L 0,5')
.attr('fill', color)
.style('stroke','none');
return "url(" + color + radius + ")";
};
/**
* sets color of circle and its links to black and removes the previous highlights
* displays overview info of node in textbox
* @param {object} node - node
*/
function click_node(node) {
d3.select(this.parentNode).raise();
fix_nodes(node);
if(to_remove){
d3.select(to_remove).selectAll(".circle").style("stroke","none")
}
to_remove = this.parentNode;
d3.select(this.parentNode).selectAll(".circle").style("stroke","black")
mark_link(node)
textbox_content(node)
reset_button_highlight()
highlight_button("overview")
}
/**
* removes the highlights of the circles and their links
*/
function click_rect() {
fix_nodes(node);
d3.selectAll(".circle").style("stroke", "none")
d3.selectAll(".link")
.style("stroke", "#999")
.attr('marker-end', function(d) {return update_marker('#999', d.target);})
text_abstract='';
text_info='';
reset_button_highlight()
document.getElementById('textbox').innerHTML = "Click node";
}
/**
* returns true if journals have a common author (self-citation)
* @param {object} source - node
* @param {object} target - node
*/
function self_citation(source,target) {
return source.author.some(item=>target.author.includes(item))
}
/**
* sets color of link (line and arrowhead) to black if it is directly connected to node
* and to grey otherwise
* @param {object} node - node
*/
function mark_link(node) {
d3.selectAll(".link")
.style("stroke", function(o) {
return is_link_for_node(node, o) ? "black" : "#999";})
.attr('marker-end', function(o) {
return is_link_for_node(node, o) ? update_marker('#000000', o.target) : update_marker('#999', o.target);})
}
/**
* returns true if link is directly connected to node and false if it is not
* @param {object} node - node
* @param {object} link - link
*/
function is_link_for_node(node, link) {
return link.source.index == node.index || link.target.index == node.index;
}
/**
* saves text for overview and abstract of node
* outputs node info to textbox
* @param {object} node - node
*/
function textbox_content(node) {
text_info = "Title:" + '</br>' + node.name +
'</br>' +'</br>'+"Author:"+ '</br>' +node.author+'</br>'+'</br>'+"Date:"+'</br>'
+node.year+'</br>'+'</br>'+"Journal:"+'</br>'+node.journal+'</br>'+'</br>'+"doi:"
+'</br>'+'<a href="'+node.doi+ '">'+node.doi+'</a>'+'</br>'+'</br>'+"Citations:"
+'</br>'+node.citations;
text_abstract = node.abstract;
document.getElementById('textbox').innerHTML = text_info;
}
/**
* sets color of btn to dark gray
* @param {object} btn - button
*/
function highlight_button(btn) {
reset_button_highlight();
document.getElementById(btn).style.background = "#CACACA";
}
/**
* sets color of all buttons to default light gray
*/
function reset_button_highlight() {
document.getElementById("overview").style.background = '';
document.getElementById("abstract").style.background = '';
}
/**
* displays abstract in textbox if a is true, overview text otherwise
* @param {bool} a- bool
*/
function display_abstract(a) {
if (text_abstract == '' && text_info == '') {
document.getElementById('textbox').innerHTML="Click node";
}
else {
if (a == true) {
document.getElementById('textbox').innerHTML = text_abstract;
}
else {
document.getElementById('textbox').innerHTML = text_info;
}
}
}
/**
* updates the positions of the links and nodes
*/
function handle_tick() {
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("transform", function (d) {return "translate(" + d.x + ", " + d.y + ")";});
}
/**
* initializes the dragging of the node
* @param {object} node - node
*/
function start_drag(node) {
d3.select(this).raise();
if (!d3.event.active)
simulation.alphaTarget(0.3).restart()
node.fx = node.x;
node.fy = node.y;
fix_nodes(node);
}
/**
* applies the dragging to the node
* @param {object} node - node
*/
function dragged(node) {
node.fx = d3.event.x;
node.fy = d3.event.y;
fix_nodes(node);
}
/**
* fix positions of all nodes except for the current node
* @param {object} this_node - node
*/
function fix_nodes(this_node) {
node.each(function(d) {
if (this_node != d) {
d.fx = d.x;
d.fy = d.y;
}
});
}
/**
* applies the transformation (zooming or dragging) to the g element
*/
function handle_zoom() {
d3.select('g').attr("transform", d3.event.transform);
}
/**
* transforms svg so that the zoom is adapted to the size of the graph
*/
function zoom_to() {
node_bounds = d3.selectAll("svg.graph").node().getBBox();
svg_bounds = d3.select("rect").node().getBBox();
perc_x = width/(node_bounds.width+100);
perc_y = height/(node_bounds.height+100);
perc = d3.min([perc_x, perc_y])
d3.select('svg')
.call(zoom.scaleBy, perc);
}
/**
* transforms svg so that the zoom and drag is reset
*/
function reset_view() {
d3.select('svg')
.call(zoom.scaleTo, 1)
d3.select('svg')
.call(zoom.translateTo, 0.5 * width, 0.5 * height);
d3.select('svg')
.call(zoom.scaleBy, perc);
}
/**
* save svg as png
*/
function save_svg(){
var svgString = get_svg_string(svg.node());
svg_string_to_image(svgString, 2*width, 2*height, 'png', save); // passes Blob and filesize String to the callback
function save( dataBlob, filesize ){
saveAs(dataBlob, 'D3 vis exported to PNG.png'); // FileSaver.js function
}
};
/**
* generate svgString
* @param {object} svgNode - node
*/
function get_svg_string(svgNode) {
svgNode.setAttribute('xlink', 'http://www.w3.org/1999/xlink');
var cssStyleText = get_css_styles(svgNode);
append_css(cssStyleText, svgNode);
var serializer = new XMLSerializer();
var svgString = serializer.serializeToString(svgNode);
svgString = svgString.replace(/(\w+)?:?xlink=/g, 'xmlns:xlink='); // Fix root xlink without namespace
svgString = svgString.replace(/NS\d+:href/g, 'xlink:href'); // Safari NS namespace fix
return svgString;
function get_css_styles(parentElement) {
var selectorTextArr = [];
// Add Parent element Id and Classes to the list
selectorTextArr.push('#' + parentElement.id);
for (var c = 0; c < parentElement.classList.length; c++)
if (!contains('.'+parentElement.classList[c], selectorTextArr))
selectorTextArr.push('.'+parentElement.classList[c]);
// Add Children element Ids and Classes to the list
var nodes = parentElement.getElementsByTagName("*");
for (var i = 0; i < nodes.length; i++) {
var id = nodes[i].id;
if (!contains('#'+id, selectorTextArr))
selectorTextArr.push('#' + id);
var classes = nodes[i].classList;
for (var c = 0; c < classes.length; c++)
if (!contains('.'+classes[c], selectorTextArr))
selectorTextArr.push('.'+classes[c]);
}
// Extract CSS Rules
var extractedCSSText = "";
for (var i = 0; i < document.styleSheets.length; i++) {
var s = document.styleSheets[i];
try {
if(!s.cssRules) continue;
} catch(e) {
if(e.name !== 'SecurityError') throw e; // for Firefox
continue;
}
var cssRules = s.cssRules;
for (var r = 0; r < cssRules.length; r++) {
if (contains(cssRules[r].selectorText, selectorTextArr))
extractedCSSText += cssRules[r].cssText;
}
}
return extractedCSSText;
function contains(str,arr) {
return arr.indexOf(str) === -1 ? false : true;
}
}
function append_css(cssText, element) {
var styleElement = document.createElement("style");
styleElement.setAttribute("type","text/css");
styleElement.innerHTML = cssText;
var refNode = element.hasChildNodes() ? element.children[0] : null;
element.insertBefore(styleElement, refNode);
}
}
/**
* convert svgString to image and export it
* @param {object} svgString - svgString
* @param {object} width - width of image
* @param {object} height - height of image
* @param {object} format - format to save image in
* @param {object} callback - callback function
*/
function svg_string_to_image( svgString, width, height, format, callback ) {
var format = format ? format : 'png';
var imgsrc = 'data:image/svg+xml;base64,'+ btoa(unescape(encodeURIComponent(svgString))); // Convert SVG string to data URL
var canvas = document.createElement("canvas");
var context = canvas.getContext("2d");
canvas.width = width;
canvas.height = height;
var image = new Image();
image.onload = function() {
context.clearRect(0, 0, width, height);
context.drawImage(image, 0, 0, width, height);
canvas.toBlob(function(blob) {
var filesize = Math.round(blob.length/1024) + ' KB';
if (callback) callback(blob, filesize);
});
};
image.src = imgsrc;
}
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<!-- style specifications for button and div elements -->
<style type="text/css">
button {
width: 100px;
height:20px;
display: flex;
justify-content: center;
position: absolute;
left: 455px;
top: 575px;
transition-duration: 0.4s;
border-radius:3px;
border:1px solid #909090;
}
.button:hover {
background-color: #CACACA;
}
button.resetZoom {
margin-left: 110px;
}
button.save {
margin-left: 220px;
}
button.abstract {
width:146px;
position:absolute;
top: 181px;
left: 1114px;
border-radius:0;
border:1px solid #909090;
}
button.overview {
width:147px;
position:absolute;
display:inline-block;
top: 181px;
left: 968px;
border-radius:0;
border:1px solid #909090;
}
div.legendbox {
width:270px;
height:170px;
padding: 10px;
/*border: 1px solid #999;*/
position: absolute;
top: 10px;
left: 968px;
display: inline-block;
margin: 0;
}
div.textbox {
width:270px;
min-height:200px;
max-height:370px;
padding: 10px;
border: 1px solid #999;
position: absolute;
top: 200px;
left: 968px;
display: inline-block;
overflow-y: scroll;
margin: 0;
}
</style>
</head>
<body>
<!-- graph -->
<svg class="graph" width="960" height="560"></svg>
<!-- legend -->
<div class="legendbox"> <svg class="legendsvg"></svg></div>
<!-- textbox -->
<div class="textbox" id = "textbox">Click node</div>
<button id="overview" class="overview" onclick='display_abstract(false), highlight_button("overview")'>Overview</button>
<button id="abstract" class="abstract" onclick='display_abstract(true), highlight_button("abstract")'>Abstract</button>
<!-- buttons -->
<button onclick="location.reload()">Reload Graph</button>
<button class="resetZoom" onclick="reset_view()">Reset View</button>
<button class="save" onclick="save_svg()">Save</button>
<!-- D3 (version 5) -->
<script src="https://d3js.org/d3.v5.min.js"></script>
<!-- scripts to save svg element as png -->
<script src="https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js"></script>
<script src="https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js"></script>
<!-- javascript for force-directed graph -->
<script type="text/javascript" id="cn" src="cn.js"></script>
</body>
</html>
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