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### =========================================================================
### H5ADMatrixSeed objects
### -------------------------------------------------------------------------
setClass("H5ADMatrixSeed",
contains=c("Array", "OutOfMemoryObject"),
representation("VIRTUAL")
)
setClass("Dense_H5ADMatrixSeed",
contains=c("H5ADMatrixSeed", "HDF5ArraySeed"),
representation(dimnames="list"),
prototype(dimnames=list(NULL, NULL))
)
setClass("CSC_H5ADMatrixSeed",
contains=c("H5ADMatrixSeed", "CSC_H5SparseMatrixSeed")
)
setClass("CSR_H5ADMatrixSeed",
contains=c("H5ADMatrixSeed", "CSR_H5SparseMatrixSeed")
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### dimnames() method for Dense_H5ADMatrixSeed objects
###
### We overwrite the method for HDF5ArraySeed objects with a method that
### accesses the slot, not the file.
setMethod("dimnames", "Dense_H5ADMatrixSeed",
function(x) S4Arrays:::simplify_NULL_dimnames(x@dimnames)
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Transposition
###
### S3/S4 combo for t.CSC_H5ADMatrixSeed
t.CSC_H5ADMatrixSeed <- function(x)
{
new2("CSR_H5ADMatrixSeed", callNextMethod())
}
setMethod("t", "CSC_H5ADMatrixSeed", t.CSC_H5ADMatrixSeed)
### S3/S4 combo for t.CSR_H5ADMatrixSeed
t.CSR_H5ADMatrixSeed <- function(x)
{
new2("CSC_H5ADMatrixSeed", callNextMethod())
}
setMethod("t", "CSR_H5ADMatrixSeed", t.CSR_H5ADMatrixSeed)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Constructor
###
.load_h5ad_rownames <- function(filepath, name="var")
{
ok <- try(h5isdataset(filepath, name), silent=TRUE)
if (isTRUE(ok)) {
## Must use rhdf5::h5read() for now, until h5mread() knows how
## to read COMPOUND datasets.
ans <- h5read(filepath, name)$index
if (!is.null(ans))
ans <- as.character(ans)
return(ans)
}
ok <- try(h5isgroup(filepath, name), silent=TRUE)
if (!isTRUE(ok))
return(NULL)
ROWNAMES_DATASET <- paste0(name, "/_index")
ok <- try(h5isdataset(filepath, ROWNAMES_DATASET), silent=TRUE)
if (!isTRUE(ok))
return(NULL)
h5mread(filepath, ROWNAMES_DATASET, as.vector=TRUE)
}
### Must return a list of length 2.
.load_h5ad_dimnames <- function(filepath)
{
ans_rownames <- .load_h5ad_rownames(filepath)
ans_colnames <- .load_h5ad_rownames(filepath, name="obs")
if (is.null(ans_rownames) && is.null(ans_colnames))
warning(wmsg("could not find dimnames in this h5ad file"))
list(ans_rownames, ans_colnames)
}
### Returns an H5ADMatrixSeed derivative (can be either a Dense_H5ADMatrixSeed,
### or a CSC_H5SparseMatrixSeed, or a CSR_H5SparseMatrixSeed object).
H5ADMatrixSeed <- function(filepath, layer=NULL)
{
if (!isSingleString(filepath))
stop(wmsg("'filepath' must be a single string specifying the ",
"path to the h5ad file"))
filepath <- file_path_as_absolute(filepath)
if (is.null(layer)) {
name <- "/X"
} else {
if (!isSingleString(layer) || layer == "")
stop(wmsg("'layer' must be NULL or a single non-empty string"))
name <- paste0("/layers/", layer)
}
if (!h5exists(filepath, name)) {
msg <- c("HDF5 object \"", name, "\" does not exist ",
"in this HDF5 file.")
if (is.null(layer))
msg <- c(msg, " Is this a valid h5ad file?")
stop(wmsg(msg))
}
dimnames <- .load_h5ad_dimnames(filepath)
if (h5isdataset(filepath, name)) {
ans0 <- HDF5ArraySeed(filepath, name)
if (length(dim(ans0)) != 2L)
stop(wmsg("HDF5 dataset \"", name, "\" in file \"", filepath, "\" ",
"does not have exactly 2 dimensions. Please consider ",
"using the HDF5Array() constructor to access this ",
"dataset."))
ans <- new2("Dense_H5ADMatrixSeed", ans0, dimnames=dimnames)
} else if (h5isgroup(filepath, name)) {
ans0 <- H5SparseMatrixSeed(filepath, name)
if (is(ans0, "CSC_H5SparseMatrixSeed"))
ans_class <- "CSC_H5ADMatrixSeed"
else
ans_class <- "CSR_H5ADMatrixSeed"
ans <- new2(ans_class, ans0, dimnames=dimnames)
} else {
stop(wmsg("HDF5 object \"", name, "\" in file \"", filepath, "\" ",
"is neither a dataset or a group. Is this a valid ",
"h5ad file?"))
}
ans
}
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