R/ICGS2toICGS1.R

In lyc-1995/DoubletDeconSeurat: Seurat wrappers with DoubletDecon

#' ICGS2_to_ICGS1
#'
#' This function converts the new ICGS2 expression file format to the ICGS1 format. In making this change, the cluster numbers (column 1 in the groups file) are retained and not the cluster names (column 2 in the groups file).
#'
#' @param rawDataFile ICGS expression or counts file (in ICGS expression file format).
#' @param groupsFile ICGS groups file.
#' @param log_file_name used for saving run notes to log file
#'
#' @return processed - data.frame of genes by samples with a row of cell clusters (column_clusters-flat) and a column of gene clusters (row_clusters-flat) when available.
#' @return groups - groups file with cell names matching the expression file.
#'
#' @keywords ICGS
#'
#' @export
#'
ICGS2toICGS1 <- function(
  rawDataFile,
  groupsFile,
  log_file_name = NULL
) {
  #pull ICGS2 header (or have it fed in)
  exp.header <- read.table(rawDataFile, sep = '\t', nrows = 1, stringsAsFactors = FALSE, row.names = 1)

  #split away the useless groups names, keep only the cell names. save new column names for later use.
  exp.header <- gsub('.*:', '', exp.header)

  #read in expression file (or have it fed in)
  exp.ICGS <- read.table(rawDataFile, sep = '\t', stringsAsFactors = FALSE, row.names = 1, header = TRUE)

  #replace the column names with the saved ones
  colnames(x = exp.ICGS) <- exp.header

  #read in the groups file (or have it fed in)
  groups.ICGS <- read.table(groupsFile, sep = '\t', stringsAsFactors = FALSE, row.names = 1, header = FALSE)

  #replace the column-clusters_flat with the first column of groups
  exp.ICGS[1, 2:ncol(x = exp.ICGS)] <- groups.ICGS[, 1]

  #split the row names into two vectors, the useless groups names and the gene names
  if (length(x = grep(':', rownames(x = exp.ICGS)[2])) == 1) {
    groups.names <- gsub(':.*', '', row.names(x = exp.ICGS))
    groups.genes <- gsub('.*:', '', row.names(x = exp.ICGS))
  } else {
    groups.names <- exp.ICGS[, 1]
    groups.genes <- row.names(exp.ICGS)
  }

  #replace the row names with the gene names
  row.names(x = exp.ICGS) <- groups.genes

  #match the useless groups names to the good groups names and put these groups into the row-clusters_flat column.
  exp.ICGS[2:nrow(x = exp.ICGS), 1] <- as.numeric(x = mapvalues(groups.names[2:length(x = groups.names)], unique(groups.names[2:length(x = groups.names)]), unique(groups.ICGS[, 1])))

  if(!is.null(log_file_name)){
    cat('ICGS2 file formatted', file = log_file_name, append = TRUE, sep = '\n')
  }
  message('ICGS2 file formatted')

  #return the new expression and groups files
  return(list(rawData = exp.ICGS, groups = groups.ICGS))
}