citation_graph.R

require(plyr)
require(XML)
require(RCurl)
require(readxl)
require(visNetwork)


# We start with a list PubMed ids, for which we would like to have the citation graph
pmids <- c(10097079)

pmids_ch <- paste(pmids, collapse=",")


citegraph <- NULL
for(pmid in pmids){
  # Get more info with the pmid id
  tryCatch({
    
    # We build the URL to retrieve the citing pmids
    path <- paste("https://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=",
                  pmid,
                  "&report=uilist&format=text&dispmax=200", sep="")
    f <- file(path)
    data <- readLines(f, warn = F)
    citing <-strsplit(xmlToList(xmlParse(data, asText = T))[1], "\n")[[1]]
    close(f)
    
    # Then we create a table containing ll these pmids
    if(length(citing) < 200){
      for(pm in citing){
        citegraph <- rbind(citegraph, data.frame(pmid=as.numeric(pmid), citing=as.numeric(pm)))
      }
    }
    
    message(paste0(pmid," done: ",length(citing)," citations"))
    
  }, warning = function(w) {
    message(w)
  }, error = function(e) {
    message(e)
  })
}


# We use visNetwork for the vizualisation of the network
# For that we need a nodes and edges tables. 

nodes <- data.frame(id=unique(c(citegraph$pmid, citegraph$citing)))
for(i in 1:nrow(nodes)){
  nodes$color[i] <- "lightblue"
  if(grepl(nodes$id[i], pmids_ch)){
    nodes$color[i] <- "red"
  }
}

edges <- data.frame(from = citegraph[,2], to = citegraph[,1])
nodes$label <- nodes$id
visNetwork(nodes, edges, width = "100%", main = "Graph network of Citation")