library(data.table)

library(tm)

library(SnowballC)

library(ggplot2)

library(wordcloud)

setwd("/afs/athena.mit.edu/user/w/i/williame/Downloads")

mt <- read.csv("sample_output_full (1).csv", header = F, stringsAsFactors = F)

setwd("/afs/athena.mit.edu/user/w/i/williame/Downloads/ClusterMetFinal2")

mtcol <- rep("f", times = nrow(mt))

mt <- cbind(mt,mtcol)

mt[] <- lapply(mt, as.character)

for (i in 1:nrow(mt)) {

  for (j in 1:ncol(mt)) {

    if (!is.na(mt[i,j])) {

      if (mt[i,j] %like% "Processing text") {

        mt[i, ncol(mt)] <- "t"

      }

    }

  }

}

n <- 1

k <- 1

p <- 1

for (i in 1:nrow(mt)) {

  if (!is.na(mt[i,ncol(mt)])) { 

    if ((mt[i,ncol(mt)] != "f") & i > n) {

      k <- i - 1

      p <- as.character(p)

      str <- paste("mt", p, ".txt", sep = "")

      write.table(as.data.frame(mt[(n+1):k,]),file = str, row.names = F, col.names = F)

      n <- k + 1

      p <- as.numeric(p)

      p <- p + 1

    }

  }

}

mt[1,ncol(mt)] != "f"

metdocs <- Corpus(DirSource("/afs/athena.mit.edu/user/w/i/williame/Downloads/ClusterMetFinal2"))

writeLines(as.character(metdocs[[25]]))

metdocs <- tm_map(metdocs,content_transformer(tolower))

toSpace <- content_transformer(function(x, pattern) { return (gsub(pattern, " ", x))})

metdocs <- tm_map(metdocs, toSpace, '"')

metdocs <- tm_map(metdocs, removeWords, stopwords("english"))

metdocs <- tm_map(metdocs, stripWhitespace)

metdocs <- tm_map(metdocs,stemDocument)

metdtm <- DocumentTermMatrix(metdocs)

metm <- as.matrix(metdtm)

rownames(metm) <- paste(substring(rownames(metm),1,3),rep("..",nrow(metm)), substring(rownames(metm), nchar(rownames(metm))-12,nchar(rownames(metm))-4))

metd <- dist(metm)

setwd("/afs/athena.mit.edu/user/w/i/williame/Downloads")

write.csv(as.matrix(metd), file ="distmatclustermetfinal2.csv")

metgroups <- hclust(metd,method="ward.D")

metgroupsplot <- as.dendrogram(metgroups)

plot(metgroups, hang=-1)

par(mfrow=c(3,1))

plot(metgroupsplot, main="Main")

plot(cut(metgroupsplot, h=100)$upper, 

     main="Upper tree of cut at h=1000")

plot(cut(metgroupsplot, h=100)$lower[[2]], 

     main="Second branch of lower tree with cut at h=1000")

library("ggplot2")

library("ggdendro")

ggdendrogram(metgroups)

metdata <- dendro_data(metgroupsplot, type = "rectangle")

head(metdata$labels)

metdatalabel<- metdata[["labels"]][["label"]]

metdatalabeldf <- as.data.frame(metdatalabel)

metdatalabeldf <- as.data.frame(cbind(metdatalabeldf, rep("n/a", times = nrow(metdatalabeldf))))

gsubmet <- function(x) {gsub("mt\\d+ .. ", "", x)}

metdatalabeldf$metdatalabel <- lapply(metdatalabeldf$metdatalabel, gsubmet)

setwd("/afs/athena.mit.edu/user/w/i/williame/Downloads/ClusterMetFinal3Text")

n <- 1

k <- 1

p <- 1

for (i in 1:nrow(mt)) {

  if (!is.na(mt[i,ncol(mt)])) { 

    if ((mt[i,ncol(mt)] != "f") & i > n) {

      k <- i - 1

      p <- as.character(p)

      str <- paste("mt", p, "text", ".txt", sep = "")

      write.table(as.data.frame(mt[n:k,]),file = str, row.names = F, col.names = F)

      n <- k + 1

      p <- as.numeric(p)

      p <- p + 1

    }

  }

}

colnames(metdatalabeldf)[c(1,2)] <- c("file", "text")

metdatalabeldf[] <- lapply(metdatalabeldf, as.character)

gsubproc <- function(x) {gsub("\'Processing text_000N_\\d+.tx.1:", "", x)}

test1 <- gsubproc(as.character(read.table(paste(metdatalabeldf[1,1],"text",".txt",sep=""), header = F)[1,2]))

for (i in 1:nrow(metdatalabeldf)) {

  metdatalabeldf[i,2] <- gsubproc(as.character(read.table(paste(metdatalabeldf[i,1],"text",".txt",sep=""), header = F, fill = T)[1,2]))

} 

setwd("/afs/athena.mit.edu/user/w/i/williame/Downloads")

write.csv(metdatalabeldf, file = "metclusterresultsclean3.csv")

pdf("pdfgraphsmetfinal1.pdf", width=40, height=15)

plot(metgroups, hang=-1)

dev.off()