R/read_plates.R

Defines functions generate_plate_names read_plates

Documented in read_plates

#' Read multiple plater-formatted files and combine result into one data frame.
#' 
#' A wrapper around \code{read_plate} that handles multiple plates and combines
#' them all into a single data frame.
#' 
#' @param files A character vector with the paths of one or more plater-formatted
#' .csv files.
#' @param plate_names A character vector the same length as \code{files} with the
#' names to give the individual plates in the resulting data frame. Defaults to
#' the file names (stripped of path and .csv). 
#' @inheritParams read_plate  
#' @return Returns a data frame like that returned by \code{read_plate}, 
#' containing the data from all of the plates. The plates will be identified 
#' with a column called "Plate" containing the names given in 
#' \code{plate_names}. 
#' 
#' @export
#' @examples 
#' # Combine multiple files into one tidy data frame
#' file1 <- system.file("extdata", "example-1.csv", package = "plater")
#' file2 <- system.file("extdata", "more-bacteria.csv", package = "plater")
#' 
#' # Data are stored in plate-shaped form
#' data <- read_plates(
#'    files = c(file1, file2),
#'    plate_names = c("Experiment 1", "Experiment 2"),
#'    well_ids_column = "Wells")
#' 
#' # Data from both plates are tidy and in the same data frame
#' head(data)
read_plates <- function(files, plate_names = NULL, well_ids_column = "Wells") {
   # check that all file paths are valid
   lapply(files, check_file_path)
   
  check_well_ids_column_name(well_ids_column)
    
   if(is.null(plate_names)) {
      plate_names <- generate_plate_names(files)
   }
   
   if(length(files) != length(plate_names)) {
      stop("files and plate_names must have the same length.")
   }
   
   list_of_data_frames <- Map(
      f = function(file, plate_name) { 
         
         tryCatch(
            expr = { 
               p <- read_plate(file, well_ids_column)
               p$Plate <- plate_name
               p
            }, 
            error = function(e) { 
               e <- paste0("Error in file '", plate_name, "': ", 
                  e$message)
               stop(e, call. = FALSE)
            })
         
      }, files, plate_names
   )
   
   result <- dplyr::bind_rows(list_of_data_frames)

   rownames(result) <- NULL
   
   # make Plate the first column instead of the last column
   result <- dplyr::select_(result, "Plate", ~ dplyr::everything())
   
   result
}

# Strip file paths and ".csv" to generate just file name as plate identifier
generate_plate_names <- function(files) {
   # remove leading file paths
   files <- regmatches(files, regexpr("[^/\\\\]*.[Cc][Ss][Vv]$", files))
   
   # remove .csv
   gsub(".[Cc][Ss][Vv]$", "", files)
}
seaaan/plateR documentation built on March 18, 2020, 7:23 p.m.