Force-Directed Diagram of Simon Goring's publication network based on DOIs and ORCiDs.

.block

license: MIT

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')

authors.json

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index.html

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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!