R/read_plate.R

In econtijoch/FaithLabTools: R Scripts for Faith Lab @ MSSM

#' Function to read in mapping file and tweak format so that it is friendly with the rest of the package functinos
#' @param plate_reader_file Fluorescence data from the plate reader (can be in .csv or .xls(x) format -- if in excel file, only the FIRST sheet within the file will be read)
#' @param size optional size of plate (96 or 384)
#' @param plate_name optional name to giv ethe plate
#' @return a list containing: 1) a data frame with the data from the plate reader file and 2) the number of measurements taken for each sample
#' @export
#'

read_plate <- function(plate_reader_file, size = 96, plate_name = NA) {


  # Import file, handle xls(x) vs csv files
  if (utils::tail(unlist(strsplit(plate_reader_file, "\\.")), n = 1) == "csv") {
    file <- readr::read_csv(plate_reader_file)
  } else if (utils::tail(unlist(strsplit(plate_reader_file, "\\.")), n = 1) == "xls" | utils::tail(unlist(strsplit(plate_reader_file,
                                                                                                                   "\\.")), n = 1) == "xlsx") {
    file <- readxl::read_excel(plate_reader_file, col_names = F)
  }


  # Find start point
  for (i in 1:(ncol(file) - 1)) {
    if (length(grep("Results", as.data.frame(file[,i])[[1]])) > 0) {
      title_row <- grep("Results", as.data.frame(file[,i])[[1]])
      if (size == 96) {
        end_row <- title_row + 11
      } else {
        end_row <- title_row + 23
      }

      start_column <- i + 2
    }
  }
  start_row = title_row + 4

  # Parse table
  parsed_table <- file[start_row:end_row, start_column:(ncol(file) - 1)]

  newtable <- data.frame(Well = NA, Measurement = NA, stringsAsFactors = FALSE)

  if (size == 96) {
    rows <- LETTERS[1:8]
    cols <- sprintf(1:12, fmt = '%02.0f')

  } else if (size == 384) {
    rows <- LETTERS[1:16]
    cols <- sprintf(1:24, fmt = '%02.0f')
  } else {
    stop('Size must be 96 or 384')
  }

  rows_length <- length(rows)
  cols_length <- length(cols)

  for (r in 1:rows_length) {
    for (c in 1:cols_length) {
      index <- (r - 1) * cols_length + c
      index_name <- paste(rows[r], cols[c], sep = "")
      newtable[index, "Well"] <- as.character(index_name)
      newtable[index, "Measurement"] <- as.numeric(as.character(parsed_table[r, c]))
    }
  }

  # Remove NAs
  final_table <- subset(newtable, !is.na(newtable$Measurement)) %>%
    dplyr::mutate(ReaderPlate = plate_name, ReaderWell = Well) %>%
    dplyr::select(ReaderPlate, ReaderWell, Measurement)

  return(final_table)

}