R/fit_gaussians.R

In fosterlab/PrInCE: Predicting Interactomes from Co-Elution

#' Fit a mixture of Gaussians to a chromatogram curve
#'
#' Fit mixtures of one or more Gaussians to the curve formed by a chromatogram
#' profile, using nonlinear least-squares. 
#' 
#' @param chromatogram a numeric vector corresponding to the chromatogram trace
#' @param n_gaussians the number of Gaussians to fit
#' @param max_iterations the number of times to try fitting the curve with
#' different initial conditions; defaults to 10
#' @param min_R_squared the minimum R-squared value to accept when fitting the
#' curve with different initial conditions; defaults to 0.5
#' @param method the method used to select the initial conditions for
#' nonlinear least squares optimization (one of "guess" or "random"); 
#' see \code{\link{make_initial_conditions}} for details
#' @param filter_gaussians_center true or false: filter Gaussians whose centres
#' fall outside the bounds of the chromatogram 
#' @param filter_gaussians_height Gaussians whose heights are below this 
#' fraction of the chromatogram height will be filtered. Setting this value to
#' zero disables height-based filtering of fit Gaussians
#' @param filter_gaussians_variance_min Gaussians whose variance falls below 
#' this number of fractions will be filtered. Setting this value to
#' zero disables filtering.
#' @param filter_gaussians_variance_max Gaussians whose variance is above
#' this number of fractions will be filtered. Setting this value to
#' zero disables filtering.
#'
#' @return a list with six entries: the number of Gaussians used to fit
#' the curve; the R^2 of the fit; the number of iterations used to 
#' fit the curve with different initial conditions; the coefficients of the 
#' fit model; and the fit curve predicted by the fit model.
#' 
#' @examples
#' data(scott)
#' chrom <- clean_profile(scott[1, ])
#' fit <- fit_gaussians(chrom, n_gaussians = 1)
#' 
#' @importFrom stats coef cor setNames nls
#' @importFrom dplyr first
#' 
#' @export
fit_gaussians <- function(chromatogram, n_gaussians,
                          max_iterations = 10, min_R_squared = 0.5,
                          method = c("guess", "random"),
                          filter_gaussians_center = TRUE,
                          filter_gaussians_height = 0.15,
                          filter_gaussians_variance_min = 0.1,
                          filter_gaussians_variance_max = 50) {
  indices <- seq_along(chromatogram)
  iter <- 0
  bestR2 <- 0
  bestCoefs <- NULL
  while (iter < max_iterations & bestR2 < min_R_squared) {
    # increment iteration counter
    iter <- iter + 1
    # make initial conditions
    initial_conditions <- make_initial_conditions(
      chromatogram, n_gaussians, method)
    A <- initial_conditions$A
    mu <- initial_conditions$mu
    sigma <- initial_conditions$sigma
    
    # fit the model
    p_model <- function(x, A, mu, sigma) {
      rowSums(sapply(seq_len(n_gaussians), 
                     function(i) A[i] * exp(-((x - mu[i])/sigma[i])^2)))
    }
    fit <- tryCatch({
      suppressWarnings(
        nls(chromatogram ~ p_model(indices, A, mu, sigma), 
            start = list(A = A, mu = mu, sigma = sigma), 
            trace = FALSE,  
            control = list(warnOnly = TRUE, minFactor = 1/2048)))
    }, error = function(e) { 
      e 
    }, simpleError = function(e) { 
      e
    })
    if ("error" %in% class(fit))
      next
    
    # split up fit coefficients vector into list with three entries
    coefs <- coef(fit)
    coefs <- split(coefs, rep(seq_len(3), each = n_gaussians))
    coefs <- setNames(coefs, c("A", "mu", "sigma"))
    
    # remove Gaussians with negative variances 
    if (filter_gaussians_variance_min > 0) {
      sigmas <- coefs[["sigma"]]
      drop <- which(sigmas < filter_gaussians_variance_min)
      if (length(drop) > 0)
        coefs <- lapply(coefs, `[`, -drop)
    }
    
    # remove Gaussians with extremely large 
    if (filter_gaussians_variance_max > 0) {
      sigmas <- coefs[["sigma"]]
      drop <- which(sigmas > filter_gaussians_variance_max)
      if (length(drop) > 0)
        coefs <- lapply(coefs, `[`, -drop)
    }
    
    # (optional): remove Gaussians outside bounds of chromatogram
    if (filter_gaussians_center) {
      means <- coefs[["mu"]]
      drop <- which(means < 0 | means > length(chromatogram))
      if (length(drop) > 0)
        coefs <- lapply(coefs, `[`, -drop)
    }
    
    # (optional): remove Gaussians less than 15% of height
    if (filter_gaussians_height > 0) {
      minHeight <- max(chromatogram) * filter_gaussians_height
      heights <- coefs[["A"]]
      drop <- which(heights < minHeight)
      if (length(drop) > 0)
        coefs <- lapply(coefs, `[`, -drop)
    }
    
    # calculate R^2
    if (length(first(coefs)) == 0)
      next
    curveFit <- fit_curve(coefs, indices)
    R2 <- cor(chromatogram, curveFit)^2
    # replace best fit with this model?
    if (R2 > bestR2 & R2 > min_R_squared) {
      bestR2 <- R2
      bestCoefs <- coefs
    }
  }
  if (!is.null(bestCoefs)) {
    curveFit <- fit_curve(bestCoefs, indices)
  } else {
    curveFit <- NULL
  }
  results <- list(n_gaussians = n_gaussians, R2 = bestR2, iterations = iter,
                  coefs = bestCoefs, curveFit = curveFit)
  return(results)
}