R/processQualitativeData.R

In nicohuttmann/htmnanalysis: Analysis of Omics Data

#' Substitutes qualitative data
#'
#' @param data data frame
#' @param name name to be saved
#' @param ... keys and values in alternating sequence
#'
#' @return
#' @export
#'
#'
processQualitativeData <- function(data, name, ...) {

  if(!hasArg(data)) {
    data <- getData()
  }

  if(hasArg(...)) {
    v <- c(...)
    keys <- vector[seq(1, length(v), 2)]
    values <- vector[seq(2, length(v), 2)]

  }

  else {

    ok <- F

    while(!ok) {

      message("Please provide a value for each key: ")

      if(is.matrix(data)) {
        keys <- unique(c(data))
      }

      else {
        keys <- unique(unlist(data))
      }


      print(keys)


      values <- c()

      #collect values
      output <- whatToDo("What type of output?", "numeric", "logical", "character")

      #numeric
      if(output == "numeric") {
        for(i in 1:length(keys)) {
          values <- c(values, getNumber(paste0("Substitute <", keys[i], "> with: ")))
        }
      }

      #logical
      if(output == "logical") {
        for(i in 1:length(keys)) {
          values <- c(values, ok(paste0("Substitute <", keys[i], "> with:")))
        }
      }

      #character
      if(output == "character") {
        for(i in 1:length(keys)) {
          values <- c(values, readline(paste0("Substitute <", keys[i], "> with: ")))
        }
      }


      names(values) <- keys

      print(values)
      message("")

      ok <- ok("Ok?")

    }

  }

  for(i in 1:length(keys)) {

    data[data == keys[i]] <- values[i]

  }

  if(!hasArg(name)) {
    name <- readline("Name of data: ")
  }


  #numeric
  if(output == "numeric") {
    data2 <- apply(data, 2, as.numeric)
    rownames(data2) <- rownames(data)
  }

  #logical
  if(output == "logical") {
    data2 <- apply(data, 2, as.logical)
    rownames(data2) <- rownames(data)
  }

  #character
  if(output == "character") {
    data2 <- apply(data, 2, as.character)
    rownames(data2) <- rownames(data)
  }




  saveThis(data2,
           name,
           "dat")

}