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### =========================================================================
### TENxMatrixSeed objects
### -------------------------------------------------------------------------
setClass("TENxMatrixSeed", contains="CSC_H5SparseMatrixSeed")
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Low-level helpers
###
.find_rownames_dataset <- function(filepath, group)
{
name <- "genes"
if (h5exists(filepath, paste(group, name, sep="/")))
return(name)
name <- "features/id"
if (h5exists(filepath, paste(group, name, sep="/")))
return(name)
NULL
}
### Return the rownames of the matrix.
.load_tenx_rownames <- function(filepath, group)
{
name <- .find_rownames_dataset(filepath, group)
if (is.null(name))
return(NULL)
read_h5sparse_component(filepath, group, name)
}
### Return the colnames of the matrix.
.load_tenx_barcodes <- function(filepath, group)
{
if (!h5exists(filepath, paste0(group, "/barcodes")))
return(NULL)
read_h5sparse_component(filepath, group, "barcodes")
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Constructor
###
TENxMatrixSeed <- function(filepath, group="matrix")
{
seed0 <- H5SparseMatrixSeed(filepath, group)
## dimnames
rownames <- .load_tenx_rownames(seed0@filepath, seed0@group)
stopifnot(is.null(rownames) || length(rownames) == seed0@dim[[1L]])
colnames <- .load_tenx_barcodes(seed0@filepath, seed0@group)
stopifnot(is.null(colnames) || length(colnames) == seed0@dim[[2L]])
dimnames <- list(rownames, colnames)
new2("TENxMatrixSeed", seed0, dimnames=dimnames)
}
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