Factory function to create a SOMA sparse ND array for writing (lifecycle: maturing).
Usage
SOMASparseNDArrayCreate(
uri,
type,
shape,
ingest_mode = c("write", "resume"),
platform_config = NULL,
tiledbsoma_ctx = NULL,
tiledb_timestamp = NULL
)Arguments
- uri
URI for the TileDB object.
- type
An Arrow type defining the type of each element in the array.
- shape
A vector of integers defining the shape of the array.
- ingest_mode
Ingestion mode when creating the TileDB object; choose from:
“
write”: create a new TileDB object and error if it already exists.“
resume”: attempt to create a new TileDB object; if it already exists, simply open it for writing.
- platform_config
Optional platform configuration.
- tiledbsoma_ctx
Optional SOMATileDBContext.
- tiledb_timestamp
Optional Datetime (POSIXct) for TileDB timestamp.
Value
A new SOMA sparse ND array
stored at uri opened for writing.
Examples
uri <- withr::local_tempfile(pattern = "soma-sparse-array")
mat <- Matrix::rsparsematrix(100L, 100L, 0.7, repr = "T")
mat[1:3, 1:5]
#> 3 x 5 sparse Matrix of class "dgTMatrix"
#>
#> [1,] -0.073 -2.80 -1.20 . 0.26
#> [2,] -0.560 -0.22 -0.74 0.33 0.28
#> [3,] -0.110 -0.11 . -0.92 1.50
(arr <- SOMASparseNDArrayCreate(uri, arrow::float64(), shape = dim(mat)))
#> <SOMASparseNDArray>
#> uri: /tmp/RtmpjD0Pq2/soma-sparse-array270963ae01ec
#> dimensions: soma_dim_0, soma_dim_1
#> attributes: soma_data
arr$write(mat)
arr$close()
(arr <- SOMASparseNDArrayOpen(uri))
#> <SOMASparseNDArray>
#> uri: /tmp/RtmpjD0Pq2/soma-sparse-array270963ae01ec
#> dimensions: soma_dim_0, soma_dim_1
#> attributes: soma_data
m2 <- arr$read()$sparse_matrix()$concat()
m2[1:3, 1:5]
#> 3 x 5 sparse Matrix of class "dgTMatrix"
#>
#> [1,] -0.073 -2.80 -1.20 . 0.26
#> [2,] -0.560 -0.22 -0.74 0.33 0.28
#> [3,] -0.110 -0.11 . -0.92 1.50