HDF5Array/R/TENxMatrixSeed-class.R at 742fb59527bce74aad0374e0b8e59a60202610fc · Bioconductor/HDF5Array · GitHub

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### =========================================================================
### TENxMatrixSeed objects
### -------------------------------------------------------------------------


setClass("TENxMatrixSeed", contains="CSC_H5SparseMatrixSeed")


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Low-level helpers
###

.find_rownames_dataset <- function(filepath, group)
{
    # features is for h5seurat.
    candidate <- c("genes", "features", "features/id")
    for(i in candidate)
    {
        if (h5exists(filepath, file.path(group, i)))
            return(i)
    }
    NULL
}

.read_h5seurat_component <- function(filepath, name){
    if (h5exists(filepath, name))
        return(as.vector(h5mread(filepath, name)))
    NULL
}

### Return the rownames of the matrix.
.load_tenx_rownames <- function(filepath, group)
{
    name <- .find_rownames_dataset(filepath, group)
    # h5seurat data location: /path/to/group/../features
    # Find dataset in altered group
    if (is.null(name)){
        group <- gsub('/[^/]+$','',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(read_h5sparse_component(filepath, group, "barcodes"))
    # h5seurat
    if (h5exists(filepath, "cell.names"))
        return(read_h5sparse_component(filepath, '', "cell.names"))
    NULL
}


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### 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)
}