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Force-Directed Diagram of Simon Goring's publication network based on DOIs and ORCiDs.
Raw
.block
license: MIT
Raw
README.md

A network plot of linked publications using DOIs and ORCiDs using D3.js based on Mike Bostock's force-directed graph here and DOI/ORCiD code initially presented here. The R back-end is a bit messy still. The hardest part was getting it into a JSON format that would work with d3.js.

Using the code on downwithtime you can append this block immediately after defining the vector of unique DOIs. It's still ugly, but it works.

to_json <- list(links = list(),
                nodes = data.frame(all.df[!duplicated(all.df$orcid),-1]))

for(i in 1:length(unique.dois)){
  doi <- unique.dois[i]
  
  authors <- all.df$name[all.df$doi %in% doi]
  
  if(length(authors) > 1){
     combi <- data.frame(t(combn(all.df$name[all.df$doi %in% unique.dois[i]], 2)),
                         width = 1)
     combi[,1] <- match(combi[,1], to_json$nodes$name)
     combi[,2] <- match(combi[,2], to_json$nodes$name)
     
  to_json$links[[i]] <- combi
  }
}

to_json$links <- do.call(rbind.data.frame, to_json$links)
colnames(to_json$links) <- c('source', 'target', 'width')

to_json$links <- to_json$links %>% group_by(source, target) %>% summarise(sum(width))
colnames(to_json$links) <- c('source', 'target', 'width')

#  There is a problem with the numbering because we don't get a consistent 1-n numbering that
#  d3 expects.
#  Here we reorder everything:

unique_source <- data.frame(news = 1:nrow(unique(to_json$links[,1])), 
                            olds = unlist(unique(to_json$links[,1])))

not_source <- to_json$links$target[!to_json$links$target %in% to_json$links$source]

target_source <- data.frame(news= 1:length(not_source) + max(unique_source$news),
                            olds = not_source)

resorter <- rbind.data.frame(unique_source, target_source)
                  
to_json$nodes <- to_json$nodes[(resorter$olds),]
to_json$links$source <- match(to_json$links$source, resorter$olds)
to_json$links$target <- match(to_json$links$target, resorter$olds)

cat(jsonlite::toJSON(to_json), file = 'authors.json')
Raw
authors.json
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Raw
index.html
<!DOCTYPE html>
<meta charset="utf-8">
<style>
.link {
fill: none;
stroke: #666;
}
circle {
fill: #ccc;
stroke: #333;
stroke-width: 1.5px;
}
simon_circle {
fill: #d8b;
stroke: #333;
stroke-width: 1.5px;
}
text {
font: 12px sans-serif;
pointer-events: none;
text-shadow: 0 1px 0 #fff, 1px 0 0 #fff, 0 -1px 0 #fff, -1px 0 0 #fff;
}
div.tooltip {
position: absolute;
text-align: center;
max-width: 200px;
height: 28px;
padding: 4px;
font: 12px sans-serif;
background: lightsteelblue;
border: 0px;
border-radius: 0px;
/* pointer-events: none; This line needs to be removed */
}
</style>
<body>
<script src="//d3js.org/d3.v3.min.js"></script>
<script>
var width = 960,
height = 500,
padding = 1.5;
var color = d3.scale.category20();
var force = d3.layout.force()
.charge(-120)
.linkDistance(30)
.size([width, height]);
// Define 'div' for tooltips
var div = d3.select("body")
.append("div") // declare the tooltip div
.attr("class", "tooltip") // apply the 'tooltip' class
.style("opacity", 0); // set the opacity to nil
var svg = d3.select("body").append("svg")
.attr("width", width)
.attr("height", height);
d3.json("https://gist.githubusercontent.com/SimonGoring/6d499c40e8f222d2146d/raw/78cc73f3c52848141ab49a9d2410bf7c77f91fc7/authors.json", function(error, graph) {
if (error) throw error;
force
.nodes(graph.nodes)
.links(graph.links)
.linkStrength(function(d){return d.source.weight / 48})
.friction(0.9)
.linkDistance(20)
.charge(-50)
.gravity(0.2)
.theta(0.8)
.alpha(0.1)
.start();
var link = svg.selectAll(".link")
.data(graph.links)
.enter().append("line")
.attr("class", "link")
.attr("stroke", "#666")
.attr("stroke-width", function(d) {
return d.source.weight / 10 + "px"; });
var node = svg.selectAll(".node")
.data(graph.nodes)
.enter().append("circle")
.attr("class", "node")
.attr("r", 5)
.call(force.drag)
.on("mouseover", mouseover)
.on("mouseout", mouseout)
.on("mousedown", clickbox);
node.append("title")
.text(function(d) { return d.name + '\n' + 'Click for ORCiD' });
// Obtain the position of the nodes & links every 'tick', as the layout
// advances through the force simulation.
// see explanation here:
// http://stackoverflow.com/questions/28745398/why-do-we-need-force-ontick-in-d3
// The simulation is '.start()'ed, it 'ticks' through and then it's `stop`ped
// although in practice we don't `stop` it.
force.on("tick", function() {
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 clickbox(d){
//d3.select(this)
// .attr("r", 16);
div.transition()
.duration(1)
.style("opacity", 0);
div.transition()
.duration(1)
.style("opacity", .9);
div.html(
'<a href= "http://orcid.org/' + d.orcid +
'" target="_blank">' + // The first <a> tag
d.orcid +
"</a>" + // closing </a> tag
"<br/>" + d.name)
.style("left", "50px")
.style("top", "50px");
}
function mouseover() {
d3.select(this).attr("r", 10);
};
function mouseout() {
d3.select(this).attr("r", 5);
};
});
</script>
@SimonGoring
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Author

Hey @BillMills I got it to work :)
http://bl.ocks.org/SimonGoring/6d499c40e8f222d2146d

A lot of it was problems with the JSON that I didn't anticipate. Partly I forgot that indexing in R is different than in js. That 0/1 thing really messed me up for a while!

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