tiledbsc 0.1.4
Features
-
Added
batch_mode
option to methods that readX
layers (i.e.,AssayMatrix
objects) into memory. When enabled, batch mode leverages the family ofBatched
classes added to tiledb-r in version 0.14.0 to detect partial query results and resubmit until all results are retrieved. This feature is currently disabled by default and only applies toX
layers (which are typically the largest arrays). You can enable batch mode from the following methods:SOMACollection$to_seurat()
SOMA$to_seurat_assay()
SOMA$to_summarized_experiment()
SOMA$to_single_cell_experiment()
AssayMatrix$to_dataframe()
AssayMatrix$to_matrix()
-
Members can now be removed from
TileDBGroup
s withremove_member()
-
New
vignette("quickstart")
which provides new users with a high-level overview of the package -
New function
dataset_seurat_pbmc3k()
to download the pbmc 3k dataset from 10X and import as aSeurat
object without requiring any extra dependencies. This dataset is used in the new vignette -
Updated bundled
Makefile
to add targets for generating pre-computed vignettes and performing common dev operations -
Added
CONTRIBUTING.md
to reference TileDB's CoC and document theMakefile
Changes
- Removed vestigial code for merging non-layerable COO data.frames, which was previously used to add ingest dense
scaled.data
from a SeuratAssay
as an attribute of theX
array, along withcounts
/data
. This is no longer necessary as each layer is now ingested into a separate array within theX
group (#73). - The internal utility
dgtmatrix_to_dataframe()
was replaced withmatrix_to_coo()
, which converts Matrix-like objects to COO data frames much more efficiently (#75). - The internal utility
pad_matrix()
can now pad a matrix by adding empty rows (#79). - The internal assertion
has_dimnames()
was replaced withis_labeled_matrix()
for clarity (#79).
Fixes
- Matrix conversion message from
AssayMatrix
now respects theverbose
option - Upon initialization
SOMA
now looks for araw
group and warns the user it will be ignored. Currently tiledbsc-py creates araw
group when converting anndata objects where.raw
is populated. However, Seurat/BioC objects do not have an obvious place to store this data, so ignoring it improves compatibility. - Fixed a non-user-facing issue with the internal
dgtmatrix_to_dataframe()
function used to convert unordereddgTMatrix
objects to COO data frames (#73). - Pretty printing of classes that inherit from
TileDBObject
has been improved so that the class name is displayed first (#79). - Don't use default assay name when recreating a
Seurat
object (#80, thanks @dan11mcguire)
Build and Test Systems
- Added
with_allocation_size_preference()
helper to temporarily set the allocation size preference for testing. - Tests were added to verify the internal
dgtmatrix_to_dataframe()
will error out if an input list contains non-layerable matrices.