tiledbsoma.ExperimentAxisQuery

class tiledbsoma.ExperimentAxisQuery(experiment: Experiment, measurement_name: str, *, obs_query: AxisQuery = AxisQuery(value_filter=None, coords=()), var_query: AxisQuery = AxisQuery(value_filter=None, coords=()), index_factory: IndexFactory = <class 'pandas.core.indexes.base.Index'>)

Axis-based query against a SOMA Experiment.

ExperimentAxisQuery allows easy selection and extraction of data from a single Measurement in an Experiment, by obs/var (axis) coordinates and/or value filter.

The primary use for this class is slicing Experiment X layers by obs or var value and/or coordinates. Slicing on SparseNDArray X matrices is supported; DenseNDArray is not supported at this time.

IMPORTANT: this class is not thread-safe.

IMPORTANT: this query class assumes it can store the full result of both axis dataframe queries in memory, and only provides incremental access to the underlying X NDArray. API features such as n_obs and n_vars codify this in the API.

The ExperimentAxisQuery is a context manager and it is recommended that you use the following pattern:

with ExperimentAxisQuery(...) as query:
    ...

Lifecycle: maturing

__init__(experiment: Experiment, measurement_name: str, *, obs_query: AxisQuery = AxisQuery(value_filter=None, coords=()), var_query: AxisQuery = AxisQuery(value_filter=None, coords=()), index_factory: IndexFactory = <class 'pandas.core.indexes.base.Index'>)

Methods

X(layer_name, *[, batch_size, partitions, ...])	Returns an X layer as a sparse read.
__init__(experiment, measurement_name, *[, ...])
close()	Releases resources associated with this query.
obs(*[, column_names, batch_size, ...])	Returns obs as an Arrow table iterator.
obs_joinids()	Returns obs soma_joinids as an Arrow array.
obs_scene_ids()	Returns a pyarrow array with scene ids that contain obs from this query.
obsm(layer)	Returns an obsm layer as a sparse read.
obsp(layer)	Returns an obsp layer as a sparse read.
to_anndata(X_name, *[, column_names, ...])	Exports the query to an in-memory AnnData object.
to_spatialdata(X_name, *[, column_names, ...])	Returns a SpatialData object containing the query results
var(*[, column_names, batch_size, ...])	Returns var as an Arrow table iterator.
var_joinids()	Returns var soma_joinids as an Arrow array.
var_scene_ids()	Return a pyarrow array with scene ids that contain var from this query.
varm(layer)	Returns a varm layer as a sparse read.
varp(layer)	Returns a varp layer as a sparse read.

Attributes

indexer	A soma_joinid indexer for both obs and var axes.
n_obs	The number of obs axis query results.
n_vars	The number of var axis query results.