R/h5_write_mat.R

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

#' write a simple matrix to a hdf5 file
#'
#' @param m matrix with > 0 rows and > 0 named columns
#' @param filename filename of hdf5 file to be written to
#' @param filepath optional, path where the file should be stored.
#' Only necessary, if the directory does not yet exist, otherwise it can
#' be supplied as part of filename
#' @return NULL, write to file

h5_write_mat <- function(m, filename, filepath = "") {
    # check input parameters
    if (is.null(m) || nrow(m) == 0 || ncol(m) == 0) {
        warning("Invalid data frame. Cannot write to file.")
        return(NULL)
    }
    if (length(colnames(m)) != ncol(m)) {
        warning("matrix needs to have proper column names.")
        return(NULL)
    }
    if (!is.character(filename) || !is.character(filepath)) {
        warning("Invalid file path. Cannot write to file.")
        return(NULL)
    }
    if (filepath != "") {
        if (!dir.exists(filepath)) {
            flag <- dir.create(filepath, recursive = TRUE)
            if (!flag) {
                warning("Could not create file path. Return without writing.")
                return(NULL)
            }
        }
    }
    # create h5 file
    if (!file.exists(filename)) {
      rhdf5::h5createFile(filename)
    }
    # write row names
    if (!is.null(rownames(m)) && !is.na(rownames(m))) {
      rhdf5::h5write(
        as.vector(rownames(m)),
        filename,
        "rownames",
        write.attributes = TRUE
      )
    }
    # write column names
    rhdf5::h5write(
      as.vector(colnames(m)),
      filename,
      "colnames",
      write.attributes = TRUE
    )
    # write matrix
    rhdf5::h5write(
      as.matrix(m),
      filename,
      "data",
      write.attributes = FALSE
    )
    return(NULL)
}