R/OLD_StandardAnalysis.R

In econtijoch/Biomass-Workflow: Microbial Density Data Generation and Analysis Tools

#' Deprecated function to process standards information and create line of best fit
#' @param standards_plate_reader_csv_file plate reader file for plate containing standards (from old machine)
#' @param standards_mapping_csv_file mapping file for plate contianing standards (for wells with standards, Type must be 'Standard')
#' @param exp_id experiment id
#' @param print print standards information or not
#' @param ... ...
#' @return list containing a table of the standards, and the information for the standard curve
#' @export
#'

Deprecated_StandardAnalysis <-
  function(standards_plate_reader_csv_file,
           standards_mapping_csv_file,
           exp_id, print = FALSE, ...) {
    # Read in raw data file from the .csv output of the plate reader. This will produce a data frame with well and read
    # information for the plate.
    rawdata <-
      Deprecated_ParsePlateReaderFile(standards_plate_reader_csv_file)
    
    # Read barcode ID's from a file containing the label information
    
    mapping <- ParseMappingFile(standards_mapping_csv_file)
    
    
    # Merge data with mapping file, label data appropriately
    data <- merge(rawdata, mapping, by = "ReaderWell")
    
    data <- subset(data, !is.na(data$BarcodeID))
    data <- subset(data, data$BarcodeID != "")
    
    rownames(data) <- data$BarcodeID
    
    
    standard_table <- split(data, data$Type)$Standard
    standard_table <-
      standard_table[order(standard_table$BarcodeID),]
    
    s_y <- standard_table$SampleMass
    s_x <- standard_table$Fluorescence
    
    standards <- data.frame(s_x, s_y)
    
    colnames(standards) <- c("x", "y")
    standard_curve <- stats::lm(standards$y ~ standards$x)
    
    scale_x <- standard_curve$coefficients[2]
    intercept <- standard_curve$coefficients[1]
    rsquared <- summary(standard_curve)$r.squared
    
    # Make Plot of Standard Curve
    standards_info <-
      paste(paste(
        "Line of best fit: Y = ",
        round(scale_x, 5),
        "* X ",
        round(intercept, 5)
      ),
      paste("R^2 = ",
            round(rsquared, 5)),
      sep = "\n")
    
    name <- paste(exp_id, "Standard Curve.pdf")
    standards_plot <-
      ggplot2::ggplot(data = standards, ggplot2::aes_string(x = "s_x", y = "s_y")) + ggplot2::geom_point(size = 4) +
      ggplot2::labs(x = "Fluorescence Measurement", y = "ug DNA in Standard", main = "Standard Curve") + ggplot2::geom_smooth(method = "lm",
                                                                                                                              se = FALSE) + ggplot2::annotate(
                                                                                                                                "text",
                                                                                                                                x = 0,
                                                                                                                                y = max(s_y),
                                                                                                                                hjust = 0,
                                                                                                                                label = standards_info
                                                                                                                              ) + EJC_theme() +
      ggplot2::theme(axis.text.x = ggplot2::element_text(
        size = 18,
        angle = 0,
        hjust = 0.5,
        color = "black"
      ))
    
    if (print == TRUE) {
      cowplot::save_plot(
        filename = name,
        plot = standards_plot,
        base_height = 6,
        base_width = 6
      )
      
      
      
      cat("Standards Information:\n")
      cat(paste(paste(
        "Line of best fit: Y = ",
        round(scale_x, 5),
        "* X ",
        round(intercept, 5)
      ), "\n", sep = ""))
      cat(paste(paste("R^2 = ", round(rsquared, 5)), "\n", sep = ""))
    }
    
    
    output_list <-
      list(
        table = standard_table,
        scale_x = scale_x,
        intercept = intercept,
        plot = standards_plot
      )
    
    return(output_list)
  }