R/h5_write_data.R

In MarianSchoen/DMC: Comparison of different Deconvolution Models in several scenarios

#' write scRNA-Seq profiles and pheno data, RNA-Seq bulk data and cell type
#' proportions within the bulks in format used by \link{benchmark} to hdf5 file
#'
#' @param sc.counts numeric matrix, with feature as rows and scRNA-Seq
#'  profiles as columns
#' @param sc.pheno data frame, with scRNA-Seq profiles as rows, and pheno
#'  entries as rows
#' @param bulk.counts numeric matrix, with features as rows bulk measurements
#'  as columns
#' @param bulk.props numeric matrix containing cell type proportions,
#'  cell types as rows, bulks as columns
#' @param filename string, where should the data be stored?
#'
#' @return NULL, function saves into ‘filename‘
#' @export

write_data <- function(
  sc.counts = NULL,
  sc.pheno = NULL,
  bulk.counts = NULL,
  bulk.props = NULL,
  filename
) {
  rhdf5::h5createFile(filename)
  # write sc counts and pheno data if present
  # assume that sc.counts and sc.pheno are never written independently...
  # in the context of this benchmark this is sensible
  if (!is.null(sc.counts) && !is.null(sc.pheno)) {
    if (length(class(sc.counts)) > 1 && !is.matrix(sc.counts))
    {
      stop("Invalid count data.")
    }
    if (length(class(sc.counts)) == 1 && !(class(sc.counts) == "dgCMatrix"))
    {
      stop("Invalid count data.")
    }
    if (!is.data.frame(sc.pheno) || is.null(rownames(sc.counts)) ||
        is.null(colnames(sc.counts)) || is.null(rownames(sc.pheno)) ||
        is.null(colnames(sc.pheno))) {
      stop("Invalid count data.")
    }
    rhdf5::h5createGroup(filename, "singlecell")
    rhdf5::h5write(
      as.vector(rownames(sc.counts)),
      filename,
      "singlecell/geneids",
      write.attributes = TRUE
    )
    rhdf5::h5write(
      as.vector(colnames(sc.counts)),
      filename,
      "singlecell/cellids",
      write.attributes = TRUE
    )
    rhdf5::h5write(
      as.matrix(sc.counts),
      filename,
      "singlecell/data",
      write.attributes = TRUE
    )
    rhdf5::h5createGroup(filename, "singlecell/pheno")
    for (name in colnames(sc.pheno)) {
      rhdf5::h5write(
        as.vector(sc.pheno[[name]]),
        filename,
        paste("singlecell/pheno", name, sep = "/")
      )
    }
  }
  # write bulks if present
  if (!is.null(bulk.counts)) {
	if (length(class(bulk.counts)) == 1) {
	    if(class(bulk.counts) != "dgCMatrix"){
     	        stop(
        	"Invalid bulk counts data (dgCMatrix). Must be matrix with colnames and rownames."
      		)
	    }
    } else {
    if (! is.matrix(bulk.counts) || is.null(rownames(bulk.counts)) || is.null(colnames(bulk.counts))) {
      stop(
        "Invalid bulk counts data (Normal Matrix). Must be matrix with colnames and rownames."
      )
    }
    }
    rhdf5::h5createGroup(filename, "bulk")
    rhdf5::h5write(
      as.vector(rownames(bulk.counts)),
      filename,
      "bulk/geneids",
      write.attributes = TRUE
    )
    rhdf5::h5write(
      as.vector(colnames(bulk.counts)),
      filename,
      "bulk/sampleids",
      write.attributes = TRUE
    )
    rhdf5::h5write(
      as.matrix(bulk.counts),
      filename,
      "bulk/data",
      write.attributes = TRUE
    )
  }
  # write bulk props if present
  if (!is.null(bulk.props)) {
    if (!is.matrix(bulk.props) || is.null(rownames(bulk.props)) ||
        is.null(colnames(bulk.props))) {
      stop(
        "Invalid bulk proportion data.
        Must be matrix with colnames and rownames."
      )
    }
    rhdf5::h5createGroup(filename, "proportions")
    rhdf5::h5write(
      as.vector(rownames(bulk.props)),
      filename,
      "proportions/celltypeids"
    )
    rhdf5::h5write(
      as.vector(colnames(bulk.props)),
      filename,
      "proportions/sampleids"
    )
    rhdf5::h5write(
      as.matrix(bulk.props),
      filename,
      "proportions/data"
    )
  }
  return(NULL)
}