R/make_tax_table.R

In jfq3/RDPutils: R Utilities for Processing RDPTool Output

make_tax_table <- function(in_file="fixrank_classified.txt", confidence=0.5) {
  #Begin with output from command line version of classifier.
  #    In this example, the example output is named "dist_03_class.txt."
  #    It is fixed rank.
  class.table <- read.table(in_file, sep="\t", fill=TRUE, stringsAsFactors=FALSE)
  
  rank.pos <- seq(from = 4, to = ncol(class.table), by = 3)
  ranks <- as.vector(class.table[1 , rank.pos])
  
  # Remove unnecessary columns
  class.table <- class.table[ , -c(2, rank.pos)]
  head(class.table)
  
  # Assign first column of class.table as row names.
  # Delete first column of class.table.
  # Sort class.table by row names.
  row.names(class.table) <- class.table[ , 1]
  class.table <- class.table[ , -1]
  class.table <- class.table[order(rownames(class.table)), ]
  
  # Fix class.table's by consolidating groups based on confidences.
  # For example, genera classified with less than specified confidence become uncl_family, etc.
  
  # Create a vector designating confidence columns
  col.no <- seq(from = 2, to = ncol(class.table), by = 2)
  
  #There may be NA's in some columns, so replace them first 
  # with confidence < specified confidence:
  for (i in 1:nrow(class.table)) {
    for (j in col.no) {
      if (is.na(class.table[i, j])) {
        class.table[i, j] <- confidence/2
      }
    }
  }
  
  #Replace IDs where first rank is unidentfied.
  first.rank <- ranks[1]
  for (i in  1:nrow(class.table)) {
    if (class.table[i, 2] < confidence) {
      class.table[i, 2] <- 1
      class.table[i, 1] <- paste("uncl", first.rank, sep = "_")
    }
  }
  
  #Replace IDs where confidence is less than specified confidence:
  col.no <- seq(from=4, to=ncol(class.table), by=2)
  for (i in 1:nrow(class.table)) {
    for (j in col.no) {
      if (class.table[i, j] < confidence) {
        class.table[i, j] <- 1
        if(substr(class.table[i, (j-3)], 1, 4)=="uncl") {class.table[i, (j-1)] <- class.table[i, (j-3)]}
        else {class.table[i, (j-1)] <- paste("uncl_", class.table[i, (j-3)], sep="")}
      }
    }
  }
  
  #Convert character columns to factors.
  i <- sapply(class.table, is.character) 
  class.table[i] <- lapply(class.table[i], as.factor) 
  
  #Remove confidence columns
  class.table <- class.table[ , -c(seq(from = 2, to = ncol(class.table), by = 2))]
  ranks <- sapply(ranks, simple_cap)
  colnames(class.table) <- ranks
  class.table <- tax_table(as.matrix(class.table), errorIfNULL=TRUE)
  return(class.table)
}