R/plotWordFreq.r

In Bohdan-Khomtchouk/geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data

#' Plots word frequencies found within gene ontology terms
#'
#' Creates barplots of word frequencies from gene ontology terms derived from either biological process (BP), cellular compartment (CC), or molecular function (MF) of genes-under-peaks that are unique between two different upstream extension levels.
#'
#'
#' @param organism Object name assigned from readGFF() command.
#' @param start Lower bound of upstream extension.
#' @param end Upper bound of upstream extension.
#' @param GOcategory Either BP, CC, or MF.
#' @param GOspecies Either org.Ag.eg.db (mosquito), org.Bt.eg.db (bovine), org.Ce.eg.db (worm), org.Cf.eg.db (canine), org.Dm.eg.db (fly), org.Dr.eg.db (zebrafish), org.Gg.eg.db (chicken), org.Hs.eg.db (human), org.Mm.eg.db (mouse), org.Mmu.eg.db (rhesus), org.Pt.eg.db (chimpanzee), org.Rn.eg.db (rat), org.Sc.sgd.db (yeast), org.Ss.eg.db (pig), or org.Xl.eg.db (frog).  
#' @param word_count Number of top words to display
#'
#' @return A barplot comprised of words sorted by frequency of occurrence from gene ontology terms of either a BP, CC, or MF category.
#'
#' @examples
#' library(rtracklayer)
#' rat <- readGFF("ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz")
#' fpath <- system.file("extdata", "somepeaksfile.txt", package="geneXtendeR")
#' peaksInput(fpath)
#' library(tm)
#' library(SnowballC)
#' library(wordcloud)
#' library(RColorBrewer)
#' library(org.Rn.eg.db)
#' plotWordFreq(rat, 0, 500, BP, org.Rn.eg.db, 10)
#'
#' @useDynLib geneXtendeR, .registration = TRUE
#'
#' @export
plotWordFreq <- function(organism, start, end, GOcategory, GOspecies, word_count) {
  if(!file.exists("peaks.txt")){
    message("Please run peaksInput() function first!  See ?peaksInput for more information")
  } else {
    oopts = options(warn=-1)
    on.exit(options(oopts))
    geneXtender <- function(upstream) {
      messy2 <- dplyr::filter(organism, type == "gene")
      neat <- dplyr::select(messy2, seqid, start, end, strand, gene_id, gene_name)
      pos_exons <- dplyr::filter(neat, strand == "+")
      neg_exons <- dplyr::filter(neat, strand == "-")
      pos_exons$start = pos_exons$start - upstream
      pos_exons$start[pos_exons$start < 0] <- 1
      pos_exons$end = pos_exons$end + 500
      neg_exons$start = neg_exons$start - 500
      neg_exons$start[neg_exons$start < 0] <- 1
      neg_exons$end = neg_exons$end + upstream
      merged_exons <- rbind(pos_exons, neg_exons)
      geneXtender.file <- dplyr::select(merged_exons, seqid, start, end, gene_id, gene_name)
      levels(geneXtender.file$seqid) <- gsub("X", "100", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chrX", "100", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("Y", "200", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chrY", "200", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("MT", "300", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chrMT", "300", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("MtDNA", "300", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chrMtDNA", "300", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("M", "300", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chrM", "300", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("Mito", "300", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chrMito", "300", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("I", "1", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr1", "1", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("II", "2", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr2", "2", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("III", "3", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr3", "3", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("IV", "4", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr4", "4", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("V", "5", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr5", "5", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("VI", "6", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr6", "6", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("VII", "7", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr7", "7", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("VIII", "8", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr8", "8", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("IX", "9", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr9", "9", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("XI", "11", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr11", "11", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("XII", "12", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr12", "12", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("XIII", "13", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr13", "13", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("XIV", "14", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr14", "14", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("XV", "15", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr15", "15", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("XVI", "16", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr16", "16", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr17", "17", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr18", "18", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr19", "19", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr20", "20", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr21", "21", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr22", "22", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr23", "23", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr24", "24", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr25", "25", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr26", "26", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr27", "27", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr28", "28", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr29", "29", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr30", "30", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr31", "31", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr32", "32", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr33", "33", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr34", "34", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr35", "35", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr36", "36", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr37", "37", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr38", "38", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr39", "39", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr40", "40", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr41", "41", levels(geneXtender.file$seqid))
      levels(geneXtender.file$seqid) <- gsub("chr42", "42", levels(geneXtender.file$seqid))
      geneXtender.file$seqid = as.numeric(as.character(geneXtender.file$seqid))
      geneXtender.sorted <- dplyr::arrange(geneXtender.file, as.numeric(seqid), start)
      write.table(geneXtender.sorted, quote = FALSE, sep = "\t", row.names = FALSE, col.names = FALSE, sprintf("geneXtender_gtf_%s.bed", upstream))
    }
    
    run2 <- function(f1, f2, peakslist) {
      .C("extractpeaks", f1, f2, peakslist)[[3]]
    }
    
    sapply(c(start, end), geneXtender)
    twogxFiles <- sprintf("geneXtender_gtf_%s.bed", c(start, end))
    linelen <- ""  
    n <- 500000
    peaksArray <- rep(linelen, n)
    peaksArray2 <- rep(linelen, n)
    cmdtmp1 <- run2(f1 = "peaks.txt", f2 = twogxFiles[[1]], as.character(peaksArray))
    cmdtmp2 <- run2(f1 = "peaks.txt", f2 = twogxFiles[[2]], as.character(peaksArray2))
    cmd1 <- cmdtmp1[cmdtmp1 != linelen]
    cmd2 <- cmdtmp2[cmdtmp2 != linelen]
    m = regexec("^(?:[^\t]+\t){3}", cmd1)
    first3.cmd1 = unlist(regmatches(cmd1, m))
    m = regexec("^(?:[^\t]+\t){3}", cmd2)
    first3.cmd2 = unlist(regmatches(cmd2, m))
    finalList = cmd2[!(first3.cmd2 %in% first3.cmd1)]
    DT <- data.table::as.data.table(do.call("rbind", strsplit(finalList, split = "\t")))
    gene_names <- DT[[8]]
    
    if (deparse(substitute(GOcategory)) == 'BP') {
      gene_names_annotated <- AnnotationDbi::select(GOspecies, gene_names, "GO", "SYMBOL")
      gene_names_annotated_DT <- as.data.table(gene_names_annotated)
      Gene <- gene_names_annotated_DT[gene_names_annotated_DT$ONTOLOGY == 'BP']
      gene <- as.data.frame(Gene)
      terms <- AnnotationDbi::select(GO.db, as.character(gene[,2]), "TERM", "GOID")
      symbol_GOID_terms <- cbind(gene$SYMBOL, terms)
      uniq_symbol_GOID_terms <- unique(symbol_GOID_terms)
    } else if (deparse(substitute(GOcategory)) == 'CC') {
      gene_names_annotated <- AnnotationDbi::select(GOspecies, gene_names, "GO", "SYMBOL")
      gene_names_annotated_DT <- as.data.table(gene_names_annotated)
      Gene <- gene_names_annotated_DT[gene_names_annotated_DT$ONTOLOGY == 'CC']
      gene <- as.data.frame(Gene)
      terms <- AnnotationDbi::select(GO.db, as.character(gene[,2]), "TERM", "GOID")
      symbol_GOID_terms <- cbind(gene$SYMBOL, terms)
      uniq_symbol_GOID_terms <- unique(symbol_GOID_terms)
    } else if (deparse(substitute(GOcategory)) == 'MF') {
      gene_names_annotated <- AnnotationDbi::select(GOspecies, gene_names, "GO", "SYMBOL")
      gene_names_annotated_DT <- as.data.table(gene_names_annotated)
      Gene <- gene_names_annotated_DT[gene_names_annotated_DT$ONTOLOGY == 'MF']
      gene <- as.data.frame(Gene)
      terms <- AnnotationDbi::select(GO.db, as.character(gene[,2]), "TERM", "GOID")
      symbol_GOID_terms <- cbind(gene$SYMBOL, terms)
      uniq_symbol_GOID_terms <- unique(symbol_GOID_terms)
      
    } else
      message("Not a valid GO category.  Must be either BP, CC, or MF.")
    
  }
  
  GO_terms <- uniq_symbol_GOID_terms$TERM
  GO_terms_corpus <- tm::Corpus(VectorSource(GO_terms))
  GO_terms_corpus <- tm::tm_map(GO_terms_corpus, removeWords, stopwords("english"))
  dtm <- tm::TermDocumentMatrix(GO_terms_corpus)
  doc_term_matrix <- as.matrix(dtm)
  v <- sort(rowSums(doc_term_matrix), decreasing = TRUE)
  d <- data.frame(word = names(v), freq = v)
  
  
  barplot(d[1:as.numeric(word_count),]$freq, 
          las = 2, 
          cex.names = 0.75, 
          names.arg = d[1:as.numeric(word_count),]$word, 
          col = "lightblue", 
          main = "Most frequent words found within GO terms", 
          ylab = "Word frequencies")
  
  
}