R/functions.R

In yanxianUCSB/yxtecanm200helper:

#' Tecan functions
#'
#' get.row.number
#' @param 
#' @keywords 
#' @export
#' @examples
#' 
#'
get.row.number <- function(workSheet, key.lookup) {
    key <- workSheet[, 1]
    return(which(key == key.lookup))
    
}

#' Tecan functions
#'
#' 
#' @param 
#' @keywords 
#' @export
#' @examples
#' 
#'
get.worksheet <- function(root) {
    worksheet <- read.csv(file = root)
    worksheet <-
        read.csv(
            file = root,
            skip = which(worksheet[, 1] == 'Time [s]') - 1,
            header = F
        )
    return(worksheet)
}

#' Tecan functions
#'
#' 
#' @param 
#' @keywords 
#' @export
#' @examples
#' 
#'
get.startTime <- function(workSheet) {
    key <- workSheet[, 1]
    time.string <- workSheet[which(key == 'Start Time:'),-1][[1]]
    values <- strptime(time.string, format = "%m/%d/%Y %I:%M:%S %p")
    if (is.na(values))
        values = strptime('7/6/2016 6:55:00 PM', format = "%m/%d/%Y %I:%M:%S %p")
    return(values)
    
}

#' Tecan functions
#'
#' 
#' @param 
#' @keywords 
#' @export
#' @examples
#' 
#'
get.time <-
    function(workSheet, startTime = get.startTime(workSheet)) {
        key <- workSheet[, 1]
        time.string <- workSheet[which(key == 'Time [s]'),-1]
        values <- startTime + as.integer(time.string)
        values <- get.minutes(values, values[1])
        return(values)
        
    }

#' Tecan functions
#'
#' 
#' @param 
#' @keywords 
#' @export
#' @examples
#' 
#'
get.minutes <- function(timeVector, timeOrigin) {
    t <- difftime(timeVector, timeOrigin, units = "mins")
    return(as.integer(t))
}

#' Tecan functions
#'
#' 
#' @param 
#' @keywords 
#' @export
#' @examples
#' 
#'
get.times <- function(workSheet) {
    key <- workSheet[, 1]
    time.string <- workSheet[which(key == 'Time [s]'),-1]
    values <- as.integer(as.character(time.string))
    return(values)
    
}

#' Tecan functions
#'
#' 
#' @param 
#' @keywords 
#' @export
#' @examples
#' 
#'
get.interval <- function(workSheet) {
    key <- workSheet[, 1]
    time.string <- workSheet[which(key == 'Interval Time'),-1][[1]]
    values <- as.integer(time.string)
    return(values)
    
}

#' Tecan functions
#'
#' 
#' @param 
#' @keywords 
#' @export
#' @examples
#' 
#'
get.temperature <- function(workSheet) {
    key <- workSheet[, 1]
    tempareture.string <-
        workSheet[which(key == 'Time [s]') + 1,-1]
    values <- as.double(tempareture.string)
    return(values)
    
}

#' Tecan functions
#'
#' 
#' @param 
#' @keywords 
#' @export
#' @examples
#' 
#'
get.intensity <- function(workSheet, row) {
    key <- workSheet[, 1]
    row.start <- which(key == 'Cycle Nr.') + 3
    if (length(row.start) == 0)
        return()
    row.end <- row.start + min(which(key[-(1:row.start)] == '')) - 1
    values <- workSheet[row.start:row.end,]
    return(values[row,-1])
    
}

#' Tecan functions
#'
#' 
#' @param 
#' @keywords 
#' @export
#' @examples
#' 
#'
get.intensities <- function(workSheet) {
    key <- workSheet[, 1]
    row.start <- which(key == 'Time [s]') + 2
    if (length(row.start) == 0)
        return()
    row.end <- row.start + min(which(key[-(1:row.start)] == '')) - 1
    values <- workSheet[row.start:row.end,]
    results <- as.data.frame(t(values[, -1]))
    output <-
        as.data.frame(sapply(results,  function(x)
            as.numeric(as.character(x))))
    return(output)
    
}

#' Tecan functions
#'
#' 
#' @param 
#' @keywords 
#' @export
#' @examples
#' 
#'
get.wells <- function(workSheet) {
    key <- workSheet[, 1]
    row.start <- which(key == 'Cycle Nr.') + 3
    if (length(row.start) == 0)
        return()
    row.end <- row.start + min(which(key[-(1:row.start)] == '')) - 1
    values <- workSheet[row.start:row.end,]
    return(values[, 1])
    
}