R/utils_Store.R

In catavallejos/BASiCS: Bayesian Analysis of Single-Cell Sequencing data

.BASiCS_MCMC_RefFreqStore <- function(Data,
                                      Chain, 
                                      RefGene,
                                      RefGenes,
                                      StoreDir,
                                      RunName) {
  
  # setwd returns current dir invisibly
  OldDir <- setwd(StoreDir)
  ## in case function exits early/fails, on.exit will return us to the right dir
  on.exit(setwd(OldDir))
  message(
    "-------------------------------------------------------------\n", 
    paste("BASiCS version", packageVersion("BASiCS"), 
    ": horizontal integration (no-spikes case)"), "\n", 
    "-------------------------------------------------------------\n"
  )
  if (length(RefGenes) == 1) {  
    message(
      "Reference gene:", RefGene + 1, "\n", 
      "Information stored as a .txt file in \n", 
      "'", StoreDir, "' directory ... \n", 
      "-------------------------------------------------------------\n"
    )
    TableRef <- cbind.data.frame(
      GeneNames = rownames(counts(Data))[RefGene + 1], 
      GeneIndex = RefGene + 1, 
      stringsAsFactors = FALSE
    )
    write.table(
      TableRef,
      paste0("TableRef_", RunName, ".txt"), 
      col.names = TRUE,
      row.names = FALSE
    )
  } else {
    message(
      "Randomly, 1 out of ", length(RefGenes), "\n",
      "genes was left as reference at each iteration \n", 
      "List of reference genes and frequencies stored as a .txt file in\n", 
      "'", StoreDir, "' directory ... \n", 
      "-------------------------------------------------------------\n"
    )
    TableRef <- cbind.data.frame(
      GeneNames = rownames(counts(Data))[RefGenes + 1], 
      GeneIndex = RefGenes + 1, 
      ReferenceFreq = Chain$RefFreq[RefGenes + 1], 
      stringsAsFactors = FALSE
    )
    write.table(
      TableRef,
      paste0("TableRef_", RunName, ".txt"), 
      col.names = TRUE,
      row.names = FALSE
    )
  }
  
}

.BASiCS_MCMC_OutputStore <- function(ChainClass,
                                     Chain,
                                     StoreChains,
                                     StoreAdapt,
                                     StoreDir,
                                     RunName) {

  # setwd returns current dir invisibly
  OldDir <- setwd(StoreDir)
  ## in case function exits early/fails, on.exit will return us to the right dir
  on.exit(setwd(OldDir))
  # Store MCMC chain
  if (StoreChains) {
    message(
      "-------------------------------------------------------------\n",
      "BASiCS_Chain object stored as ",
      paste0("chain_", RunName, ".Rds"), " file in", "\n",
      paste0("'", StoreDir, "' directory ... "), "\n",
      "-------------------------------------------------------------\n"
    )
    saveRDS(ChainClass, file = paste0("chain_", RunName, ".Rds"))
  }
  # Store adaptive variances
  if (StoreAdapt) {
    message(
      "-------------------------------------------------------------\n",
      "Storing trajectories of adaptive proposal variances (log-scale) as",
      "chain_ls_", RunName, ".Rds file in \n",
      "'", StoreDir, "' directory ... \n",
      "-------------------------------------------------------------\n"
    )
    ChainLS <- list(
      ls.mu = Chain$ls.mu,
      ls.delta = Chain$ls.delta,
      ls.nu = Chain$ls.nu,
      ls.theta = Chain$ls.theta
    )
    if ("ls.phi" %in% names(Chain)) {
      ChainLS$ls.phi <- Chain$ls.phi
    }
    saveRDS(ChainLS, file = paste0("chain_ls_", RunName, ".Rds"))
  }
}