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#' Read a DataFrame factor from disk
#'
#' Read a \linkS4class{DataFrameFactor} from its on-disk representation.
#' This is usually not directly called by users, but is instead called by dispatch in \code{\link{readObject}}.
#'
#' @param path String containing a path to a directory, itself created with the \code{\link{saveObject}} method for \linkS4class{DataFrameFactor}s.
#' @param metadata Named list containing metadata for the object, see \code{\link{readObjectFile}} for details.
#' @param ... Further arguments to pass to internal \code{\link{altSaveObject}} calls.
#'
#' @return A \linkS4class{DataFrameFactor} represented by \code{path}.
#'
#' @author Aaron Lun
#'
#' @seealso
#' \code{"\link{saveObject,DataFrameFactor-method}"}, for the staging method.
#'
#' @examples
#' library(S4Vectors)
#' df <- DataFrame(X=LETTERS[1:5], Y=1:5)
#' out <- DataFrameFactor(df[sample(5, 100, replace=TRUE),,drop=FALSE])
#'
#' tmp <- tempfile()
#' saveObject(out, tmp)
#' readObject(tmp)
#'
#' @export
#' @aliases loadDataFrameFactor
#' @importFrom S4Vectors DataFrameFactor
readDataFrameFactor <- function(path, metadata, ...) {
fpath <- file.path(path, "contents.h5")
fhandle <- H5Fopen(fpath, flags="H5F_ACC_RDONLY")
on.exit(H5Fclose(fhandle), add=TRUE, after=FALSE)
host <- "data_frame_factor"
ghandle <- H5Gopen(fhandle, host)
on.exit(H5Gclose(ghandle), add=TRUE, after=FALSE)
codes <- .simple_read_codes(ghandle)
levels <- altReadObject(file.path(path, "levels"), ...)
output <- DataFrameFactor(index=codes, levels=levels)
if (h5_object_exists(ghandle, "names")) {
names(output) <- h5_read_vector(ghandle, "names")
}
readMetadata(
output,
metadata.path=file.path(path, "other_annotations"),
mcols.path=file.path(path, "element_annotations"),
...
)
}
#######################################
########### OLD STUFF HERE ############
#######################################
#' @export
loadDataFrameFactor <- function(info, project, ...) {
lev.info <- acquireMetadata(project, info$data_frame_factor$levels$resource$path)
levels <- altLoadObject(lev.info, project=project)
path <- acquireFile(project, info$path)
has.names <- isTRUE(info$factor$names)
idx <- .quickReadCsv(path,
c(index="integer"),
row.names=has.names,
compression=info$factor$compression,
expected.nrows=info$factor$length
)
indexes <- idx$index
if (has.names) {
names(indexes) <- rownames(idx)
}
DataFrameFactor(index=indexes, levels=levels)
}
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