R/Spectra_Constructors.R

In julianstanley/SensorOverlord: A Tyrant of Absolute Quantitative Ratiometric Microscopy

# sensorSpectra constructors -----

#' A function to make a sensorSpectra from a set of 4 vectors
#'
#' I'll typically collect spectra data in an excel file with 4 columns:
#' the lambda and emission  values corresponding to the minimum and
#' maximum states. This function takes data from those 4 columns, condenses
#' them into a 3-column dataframe (with matching lambda values), and makes
#' a sensorSpectra object
#'
#' @param lambdas_minimum Lambdas of the values corresponding to the Rmin state
#' @param values_minimum Emission values corresponding to the Rmin state
#' @param lambdas_maximum Lambdas of the values corresponding to the Rmax state
#' @param values_maximum Emission values corresponding to the Rmax state

#' @return A sensorSpectra object
#'
#' @export
#' @rdname spectraMatrixFromValues-function
#' @import stats
spectraMatrixFromValues <- function(lambdas_minimum,
                                    values_minimum,
                                    lambdas_maximum,
                                    values_maximum) {
    # Trim any NA values
    lambdas_minimum <- na.omit(lambdas_minimum)
    values_minimum <- na.omit(values_minimum)
    lambdas_maximum <- na.omit(lambdas_maximum)
    values_maximum <- na.omit(values_maximum)

    # Set beginning and ending lambda values
    # Warning: will trim lambdas not in the range of shared values
    start <- max(min(lambdas_minimum),
                 min(lambdas_maximum))
    end <- min(max(lambdas_minimum),
               max(lambdas_maximum))
    range <- seq(start, end, by = 0.1)

    new_values_minimum <- rescaleToRange(new_xs = range,
                                         old_xs = lambdas_minimum,
                                         y = values_minimum)
    new_values_maximum <- rescaleToRange(new_xs = range,
                                         old_xs = lambdas_maximum,
                                         y = values_maximum)

    return(
        new(
            "sensorSpectra",
            lambdas = range,
            values_minimum = new_values_minimum,
            values_maximum = new_values_maximum
        )
    )

}