SOMA Blockwise Read Iterator for Sparse Matrices

Class that allows for blockwise read iteration of SOMA reads as sparse matrices.

Super classes

tiledbsoma::ReadIter -> tiledbsoma::BlockwiseReadIterBase -> BlockwiseSparseReadIter

Active bindings

repr

Representation of the sparse matrix to return.

Methods

Public methods

• BlockwiseSparseReadIter$new()

• BlockwiseSparseReadIter$concat()

• BlockwiseSparseReadIter$clone()

Inherited methods

• tiledbsoma::BlockwiseReadIterBase$read_complete()
• tiledbsoma::BlockwiseReadIterBase$read_next()

---

Method new()

Create.

Usage

BlockwiseSparseReadIter$new(
  sr,
  array,
  coords,
  axis,
  ...,
  repr = "T",
  reindex_disable_on_axis = NA
)

Arguments

sr

SOMA read pointer

array

Underlying SOMASparseNDArray

coords

Named list of CoordsStrider objects; must be named after array$dimnames()

axis

Axis to iterate over in a blockwise manner

...

Ignored

repr

Representation of the sparse matrix to return; choose from:

• “T”: returns a TsparseMatrix

• “R”: returns an RsparseMatrix

• “C”: returns a CsparseMatrix

Note: passing repr of “R” or “C” are only available if re-indexing is enabled on axes 0 or 1, respectively

reindex_disable_on_axis

Additional axes that will not be re-indexed; the following values may be used as shorthands for common settings:

• “TRUE”: disable re-indexing on all axes

• “NA”: re-index only on axis, disable re-indexing on all others

• “FALSE”: re-index on all axes, do not disable re-indexing

---

Method concat()

Concatenate the remainder of the blockwise iterator.

Usage

BlockwiseSparseReadIter$concat()

Returns

A sparse matrix (determined by self$repr) with the remainder of the iterator.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

BlockwiseSparseReadIter$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

dir <- withr::local_tempfile(pattern = "blockwise-matrix")
dir.create(dir, recursive = TRUE)
(exp <- load_dataset("soma-exp-pbmc-small", dir))
#> <SOMAExperiment>
#>   uri: /tmp/RtmpjD0Pq2/blockwise-matrix27092490ffab/soma-exp-pbmc-small
qry <- exp$axis_query("RNA")
xqry <- qry$X("data")

iter <- xqry$blockwise(0L, size = 20L, reindex_disable_on_axis = TRUE)$sparse_matrix()
stopifnot(inherits(iter, "BlockwiseSparseReadIter"))

while (!iter$read_complete()) {
  block <- iter$read_next()
}