R/36-MFA.R

In duohongrui/simmethods: A collection of 40+ simulation methods for singlce-cell RNA seqencing data

#' Estimate Parameters From Real Datasets by MFA
#'
#' This function is used to estimate useful parameters from a real dataset by
#' using \code{splatEstimate} function in Splatter package.
#'
#' @param ref_data A count matrix. Each row represents a gene and each column
#' represents a cell.
#' @param verbose Logical.
#' @param seed An integer of a random seed.
#' @importFrom peakRAM peakRAM
#' @importFrom splatter mfaEstimate
#' @return A list contains the estimated parameters and the results of execution
#' detection.
#' @export
#' @references
#' Campbell K R, Yau C. Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers. Wellcome open research, 2017, 2. <https://doi.org/10.12688/wellcomeopenres.11087.1>
#'
#' Github URL: <https://github.com/kieranrcampbell/mfa>
#'
#' @examples
#' \dontrun{
#' ref_data <- simmethods::data
#' ## estimation
#' estimate_result <- simmethods::MFA_estimation(
#'   ref_data = ref_data,
#'   verbose = TRUE,
#'   seed = 111
#' )
#' }
#'
MFA_estimation <- function(ref_data,
                           verbose = FALSE,
                           seed){

  ##############################################################################
  ####                            Environment                                ###
  ##############################################################################
  if(!requireNamespace("splatter", quietly = TRUE)){
    message("Splatter is not installed on your device")
    message("Installing splatter...")
    BiocManager::install("splatter")
  }
  ##############################################################################
  ####                               Check                                   ###
  ##############################################################################
  if(!is.matrix(ref_data)){
    ref_data <- as.matrix(ref_data)
  }
  ##############################################################################
  ####                            Estimation                                 ###
  ##############################################################################
  if(verbose){
    message("Estimating parameters using MFA")
  }
  # Seed
  set.seed(seed)
  # Estimation
  estimate_detection <- peakRAM::peakRAM(
    estimate_result <- splatter::mfaEstimate(ref_data)
  )
  ##############################################################################
  ####                           Ouput                                       ###
  ##############################################################################
  estimate_output <- list(estimate_result = estimate_result,
                          estimate_detection = estimate_detection)
  return(estimate_output)
}


#' Simulate Datasets by MFA
#'
#' @param parameters A object generated by [splatter::mfaEstimate()]
#' @param other_prior A list with names of certain parameters. Some methods need
#' extra parameters to execute the estimation step, so you must input them. In
#' simulation step, the number of cells, genes, groups, batches, the percent of
#' DEGs are usually customed, so before simulating a dataset you must point it out.
#' See `Details` below for more information.
#' @param return_format A character. Alternative choices: list, SingleCellExperiment,
#' Seurat, h5ad. If you select `h5ad`, you will get a path where the .h5ad file saves to.
#' @param verbose Logical. Whether to return messages or not.
#' @param seed A random seed.
#' @importFrom splatter mfaSimulate
#' @export
#' @details
#' #' @details
#' In MFA, users can only set `nCells` and `nGenes` to specify the number of cells and genes in the
#' simulated dataset. See `Examples` for instructions.
#'
#' For more customed parameters, see [splatter::MFAParams()] and [splatter::mfaSimulate()].
#'
#' @references
#' Campbell K R, Yau C. Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers. Wellcome open research, 2017, 2. <https://doi.org/10.12688/wellcomeopenres.11087.1>
#'
#' Github URL: <https://github.com/kieranrcampbell/mfa>
#'
#' @examples
#' \dontrun{
#' ref_data <- simmethods::data
#' ## estimation
#' estimate_result <- simmethods::MFA_estimation(
#'   ref_data = ref_data,
#'   verbose = TRUE,
#'   seed = 111
#' )
#'
#' # 1) Simulate with default parameters
#' simulate_result <- simmethods::MFA_simulation(
#'   parameters = estimate_result[["estimate_result"]],
#'   other_prior = NULL,
#'   return_format = "list",
#'   verbose = TRUE,
#'   seed = 111
#' )
#' ## counts
#' counts <- simulate_result[["simulate_result"]][["count_data"]]
#' dim(counts)
#'
#' # 2) 5000 cells and 5000 genes
#' simulate_result <- simmethods::MFA_simulation(
#'   parameters = estimate_result[["estimate_result"]],
#'   other_prior = list(nCells = 5000,
#'                      nGenes = 5000),
#'   return_format = "list",
#'   verbose = TRUE,
#'   seed = 111
#' )
#'
#' ## counts
#' counts <- simulate_result[["simulate_result"]][["count_data"]]
#' dim(counts)
#' }
#'
MFA_simulation <- function(parameters,
                           other_prior = NULL,
                           return_format,
                           verbose = FALSE,
                           seed
){

  ##############################################################################
  ####                            Environment                                ###
  ##############################################################################
  if(!requireNamespace("splatter", quietly = TRUE)){
    message("Splatter is not installed on your device")
    message("Installing splatter...")
    BiocManager::install("splatter")
  }
  ##############################################################################
  ####                               Check                                   ###
  ##############################################################################
  assertthat::assert_that(class(parameters) == "MFAParams")
  if(!is.null(other_prior)){
    parameters <- simutils::set_parameters(parameters = parameters,
                                           other_prior = other_prior,
                                           method = "MFA")
  }

  # Get params to check
  params_check <- splatter::getParams(parameters, c("nCells",
                                                    "nGenes"))

  # Return to users
  message(paste0("nCells: ", params_check[['nCells']]))
  message(paste0("nGenes: ", params_check[['nGenes']]))
  ##############################################################################
  ####                            Simulation                                 ###
  ##############################################################################
  if(verbose){
    message("Simulating datasets using MFA")
  }
  # Seed
  parameters <- splatter::setParam(parameters, name = "seed", value = seed)
  # Estimation
  simulate_detection <- peakRAM::peakRAM(
    simulate_result <- splatter::mfaSimulate(parameters,
                                             verbose = verbose)
  )
  ##############################################################################
  ####                        Format Conversion                              ###
  ##############################################################################
  simulate_result <- simutils::data_conversion(SCE_object = simulate_result,
                                               return_format = return_format)

  ##############################################################################
  ####                           Ouput                                       ###
  ##############################################################################
  simulate_output <- list(simulate_result = simulate_result,
                          simulate_detection = simulate_detection)
  return(simulate_output)
}