R/fitGP.R

In ococrook/bandle: An R package for the Bayesian analysis of differential subcellular localisation experiments

##' The \code{fitGP} function is a helper function to fit GPs with squared
##' exponential co-variances, maximum marginal likelihood
##' 
##' @title Fit a Gaussian process to spatial proteomics data
##' @param object A instance of class `MSnset`
##' @param fcol A feature column indicating markers. Default is markers.
##' @md
##' @examples 
##' library(pRolocdata)
##' data("tan2009r1")
##' set.seed(1)
##' tansim <- sim_dynamic(object = tan2009r1, 
##'                     numRep = 6L,
##'                    numDyn = 100L)
##' gpParams <- lapply(tansim$lopitrep, function(x) fitGP(x))
##'
##'@rdname bandle-gpfit
fitGP <- function(object = object,
                  fcol = "markers") {

  stopifnot("object is not an instance of class MSnSet"=is(object, "MSnSet"))    
    
    
  ## storage
  componenthypers <- vector(mode = "list", length(getMarkerClasses(object, fcol = fcol)))

  ## required quantities
  D <- ncol(object)
  K <- length(getMarkerClasses(object, fcol = fcol))

  # random grid sampling for starting values
  initialvalues <- seq(-3, 3, 2)
  init <- matrix(0, length(initialvalues), 3)
  for(i in seq_along(initialvalues)){
    init[i, ] <- initialvalues[sample.int(length(initialvalues), size = 3, replace = TRUE)]
  }

  # indexing sets
  idx <- seq.int(D)
  tau <- seq.int(D)

  # LBFGS routine to get hypers via maximum marginal likelihood
  for (j in seq.int(K)) {
    
    exprs <- t(Biobase::exprs(object[fData(object)[, fcol] == getMarkerClasses(object,
                                                                      fcol = fcol)[j], idx]))
    
    res <- apply(init, 1, function(z){lbfgs(likelihoodGP,
                                            gradientGP,
                                            vars = z,
                                            invisible = 1,
                                            epsilon = 1e-8,
                                            Xk = exprs,
                                            tau =  seq.int(D),
                                            nk = length(exprs)/D,
                                            D = D)})
    componenthypers[[j]] <- res[[which.min(lapply(res, function(x){max(x$value)}))]]$par
  }

  # store hyperparamters
 .hypers <- matrix(unlist(componenthypers), ncol = 3, byrow = TRUE)

  # get hyperparamters
  lk <- exp(.hypers[,1])
  ak <- exp(2 * .hypers[,2])
  sigma <- exp(2 * .hypers[,3])
  M <- vector(mode = "list", K)
  V <- vector(mode = "list", K)
  Var <- vector(mode = "list", K)

  # plotting routine 
  for(j in seq.int(K)){
    Orgdata <- t(Biobase::exprs(object[fData(object)$markers == getMarkerClasses(object)[j],idx]))
     matplot(x = idx, Orgdata, col = getStockcol()[j], pch = 19, type = "b", lty = 1, lwd = 1.5,
             main = paste(getMarkerClasses(object, fcol = fcol)[j]),
            xlab = "Fraction", ylab = "Normalised Abundance", cex.main = 2,
            ylim = c(min(Orgdata) - 0.05, max(Orgdata) + 0.05), cex.axis = 1.5, cex.main = 1.5, 
            xaxt = "n", axes = FALSE)
     axis(2)
     axis(1, at = idx, labels = idx)
    
    # basic paramters
    nk <- table(fData(object)$markers)[getMarkerClasses(object, fcol = fcol)][j]
    S <- matrix(rep(seq.int(length(tau)), length(tau)), nrow = length(tau))
    params <- .hypers
    sigmak <- sigma[j]
    a <- ak[j]
    l <- lk[j]
    
    #trench computations
    covA <- a * exp( - (S - t(S))^ 2 / l)
    R <- diag(1, D) + (nk * covA)/sigmak;
    trenchres <- trenchDetcpp(R[1,])
    Z <- trenchInvcpp(trenchres$v)
    invcov <- diag(1, nk*D)/sigmak - kronecker(matrix(1, nk, nk), Z %*% covA)/sigmak^2
    Kstar <- a*exp(-(matrix(rep(tau, nk * D),  nrow = D, byrow = FALSE) - matrix(rep(tau, nk*D),nrow = D, byrow = TRUE))^2/l)
    Kstarstar <- rep(a+sigmak, length(tau))
    M[[j]] <- Kstar %*% invcov %*% as.vector(Orgdata)
    V[[j]] <- as.matrix(sqrt(diag(diag(Kstarstar, length(tau)) - Kstar %*% invcov %*% t(Kstar))))
    Var[[j]] <- diag(rep(a, length(tau))) - Kstar %*% invcov %*% t(Kstar)
    
    # plotting terms
    points(seq_along(tau), M[[j]], col = "black", pch = 19,
           cex = 1.3, type = "b", lwd = 5, lty = 1)
    arrows(seq_along(tau), M[[j]]-1.96*V[[j]],
           seq_along(tau), M[[j]]+1.96*V[[j]], length=0.1,
           angle=90, code=3, col = "black", lwd = 3)
  }

  # output
  .res <- .gpParams(method = "fitGP",
                    M = M, 
                    V = V, 
                    sigma = sigma, 
                    params = params)

  return(.res)
  
}