R/rac_process_titers.R

In Racmacs: Antigenic Cartography Macros

#' Read in a table of titer data
#'
#' Reads in a table of titer data, converting it to a matrix of titers with
#' labelled column and row names. Missing titers should be represented by an
#' asterisk character.
#'
#' @param filepath Path to the table of titer data
#'
#' @returns Returns a matrix of titers.
#' @details Currently supported file formats are .csv and .xls and .txt
#' @family functions for working with map data
#' @export
#'
read.titerTable <- function(filepath) {

  if (grepl("\\.csv$", filepath)) {

    # Read from csv
    titer_table <- utils::read.csv(
      file             = filepath,
      row.names        = 1,
      check.names      = FALSE,
      stringsAsFactors = FALSE,
      colClasses       = "character"
    )

  } else if (grepl("\\.xls$", filepath) | grepl("\\.xlsx$", filepath)) {

    # Check gdata package installed
    package_required("readxl")

    # Read from xls
    titer_table_tibble <- readxl::read_excel(
      path = filepath,
      col_types = "text",
      .name_repair = "minimal"
    )

    # Convert to a character matrix
    titer_table <- as.matrix(titer_table_tibble[,-1])
    rownames(titer_table) <- titer_table_tibble[[1]]

  } else if (grepl("\\.txt$", filepath)) {

    # Read from tab delimted txt
    fileLines <- readLines(filepath, warn = FALSE)

    # Ignore lines starting with ;
    fileLines <- fileLines[!grepl("^;", fileLines)]

    # Read line content
    rows <- lapply(
      fileLines,
      function(x) {
        scan(text = x, what = "c", quiet = TRUE)
      }
    )

    # Remove empty rows
    rows <- rows[sapply(rows, length) > 0]

    # Identify any header rows
    rowlengths  <- sapply(rows, length)
    header_rows <- which(rowlengths < max(rowlengths))

    # Bind the data into a table
    titer_table <- do.call(rbind, rows[-header_rows])

    # Take row names from the first column
    rownames(titer_table) <- titer_table[, 1]
    titer_table <- titer_table[, -1]

    # Apply column names
    colnames(titer_table) <- rows[[header_rows[1]]]

  } else {

    # Unsupported filetype
    stop("File type '", tools::file_ext(filepath), "' not supported.")

  }

  # Convert to matrix
  titer_table <- as.matrix(titer_table)

  # Convert to character
  mode(titer_table) <- "character"

  # Trim white space
  titer_table <- trimws(titer_table)

  # Replace blanks with "*"
  if (sum(titer_table == "") > 0) {
    titer_table[titer_table == ""] <- "*"
    warning(
      'Missing values ("*") introduced into HI table by coercion.',
      call. = FALSE
    )
  }

  # Return HI table
  titer_table

}