dendrogramming.R

setwd("/Users/Aron/Dropbox/Projects/dendrogramming/")
library(TraMineR)
library(dendextend)
library(pvclust)
set.seed(1L)

generate <- read.csv(file = "MEP_R_Generate.csv", header = TRUE)
negotiate <- read.csv(file = "MEP_R_Negotiate.csv", header = TRUE)
transfer <- read.csv(file = "MEP_R_Transfer.csv", header = TRUE)
validate <- read.csv(file = "MEP_R_Validate.csv", header = TRUE)

generate_dendrogram <- function(data, name){
  row.names(data) <- data$id
  data.seq <- seqdef(data[2:ncol(data)], right = "DEL")
  ccost2 <- seqsubm(data.seq, method = "CONSTANT", cval = 2, with.missing=TRUE)
  data.dist <- seqdist(data.seq, method = "OM", norm = TRUE, sm = ccost2, with.missing=TRUE)
  rownames(data.dist) <- gsub(name, "", rownames(data.seq))
  colnames(data.dist) <- gsub(name, "", rownames(data.seq))
  par(mfrow = c(1,1))
  result <- pvclust(data.dist, method.dist = "abscor", method.hclust = "ward", nboot=100)
  # with pvrect
  # plot(result, main = name)
  # pvrect(result)
  # with a dendrogram of pvrect
  dend <- as.dendrogram(result, edge.root = FALSE)
  result %>% as.dendrogram(edge.root = FALSE) %>% 
    plot(main = paste("Cluster dendrogram with AU/BP values (%)\n reproduced plot with dendrogram", name))
  result %>% text
  result %>% pvrect
}

generate_dendrogram(generate, "Generate")
generate_dendrogram(negotiate, "Negotiate")
generate_dendrogram(transfer, "Transfer")
generate_dendrogram(validate, "Validate")