R/thetaAligned.R

In PratheepaJ/diffTop: Differential topic analysis using latent Dirichlet allocation

#' Align topic proportions in specimens across chain.
#'
#' @param theta array. three dimensional array (iterations * topic * specimens).
#' @param aligned aligned matrix. A matrix of topic assignment for each chain. output of alignmentMatrix.
#' @inheritParams alignmentMatrix
#'
#' @return array. three dimensional array.
#' @export
#'

thetaAligned <- function(theta,
                         K,
                         aligned,
                         iterUse = 1000,
                         chain = 4){
  # align topics between chains
  # switch samples and Topic dimension in array
  theta <- aperm(theta, c(1,3,2))

  theta_chain <- list()
  theta_chain[[1]] <- theta[1:(iterUse), ,]
  theta_chain[[1]] <- theta_chain[[1]][, aligned[,1],]

  for(ch in 2:chain){
    theta_chain[[ch]] <- theta[((ch-1)*(iterUse)+1):(ch*(iterUse)),,]
    theta_chain[[ch]] <- theta_chain[[ch]][,aligned[,ch],]
  }

  theta_aligned <- abind(theta_chain[[1]], theta_chain[[2]], along = 1)
  for(ch in 3:chain){
    theta_aligned <- abind(theta_aligned, theta_chain[[ch]], along = 1)
  }
  # switch back samples and Topic dimension in array
  theta_aligned <- aperm(theta_aligned, c(1,3,2))


  return(theta_aligned)
}