diff --git a/_autosummary/cellxgene_census.download_source_h5ad.html b/_autosummary/cellxgene_census.download_source_h5ad.html index 9b6b70c7b..0fe56194c 100644 --- a/_autosummary/cellxgene_census.download_source_h5ad.html +++ b/_autosummary/cellxgene_census.download_source_h5ad.html @@ -123,13 +123,6 @@ - - -
- 1.16.2 -
- -
@@ -223,7 +216,7 @@

cellxgene_census.download_source_h5ad

-cellxgene_census.download_source_h5ad(dataset_id: str, to_path: str, *, census_version: str = 'stable', progress_bar: bool = True) → None
+cellxgene_census.download_source_h5ad(dataset_id: str, to_path: str, *, census_version: str = 'stable', progress_bar: bool = True) → None

Download the source H5AD dataset, for the given dataset_id, to the user-specified file name.

@@ -236,7 +229,7 @@

cellxgene_census.download_source_h5adRaises: -

ValueError – if the path already exists (i.e., will not overwrite an existing file), or is not a file.

+

ValueError – if the path already exists (i.e., will not overwrite an existing file), or is not a file.

Lifecycle

diff --git a/_autosummary/cellxgene_census.experimental.get_all_available_embeddings.html b/_autosummary/cellxgene_census.experimental.get_all_available_embeddings.html index 3b55ee915..2f0fef1c1 100644 --- a/_autosummary/cellxgene_census.experimental.get_all_available_embeddings.html +++ b/_autosummary/cellxgene_census.experimental.get_all_available_embeddings.html @@ -123,13 +123,6 @@ - - -
- 1.16.2 -
- -
@@ -224,7 +217,7 @@

cellxgene_census.experimental.get_all_available_embeddings

-cellxgene_census.experimental.get_all_available_embeddings(census_version: str) → list[dict[str, Any]]
+cellxgene_census.experimental.get_all_available_embeddings(census_version: str) → list[dict[str, Any]]

Return a dictionary of all available embeddings for a given Census version.

Parameters:
diff --git a/_autosummary/cellxgene_census.experimental.get_all_census_versions_with_embedding.html b/_autosummary/cellxgene_census.experimental.get_all_census_versions_with_embedding.html index fea6bc5cc..9ea40a1dd 100644 --- a/_autosummary/cellxgene_census.experimental.get_all_census_versions_with_embedding.html +++ b/_autosummary/cellxgene_census.experimental.get_all_census_versions_with_embedding.html @@ -123,13 +123,6 @@ - - -
- 1.16.2 -
- -
@@ -224,7 +217,7 @@

cellxgene_census.experimental.get_all_census_versions_with_embedding

-cellxgene_census.experimental.get_all_census_versions_with_embedding(embedding_name: str, organism: str, embedding_type: str | None = 'obs_embedding') → list[str]
+cellxgene_census.experimental.get_all_census_versions_with_embedding(embedding_name: str, organism: str, embedding_type: str | None = 'obs_embedding') → list[str]

Get a list of all census versions that contain a specific embedding.

Parameters:
diff --git a/_autosummary/cellxgene_census.experimental.get_embedding.html b/_autosummary/cellxgene_census.experimental.get_embedding.html index 5d4f2ae7c..30abf7fe3 100644 --- a/_autosummary/cellxgene_census.experimental.get_embedding.html +++ b/_autosummary/cellxgene_census.experimental.get_embedding.html @@ -123,13 +123,6 @@ - - -
- 1.16.2 -
- -
@@ -224,7 +217,7 @@

cellxgene_census.experimental.get_embedding

-cellxgene_census.experimental.get_embedding(census_version: str, embedding_uri: str, obs_soma_joinids: ndarray[Any, dtype[int64]] | Array, context: SOMATileDBContext | None = None) → ndarray[Any, dtype[float32]]
+cellxgene_census.experimental.get_embedding(census_version: str, embedding_uri: str, obs_soma_joinids: ndarray[Any, dtype[int64]] | Array, context: SOMATileDBContext | None = None) → ndarray[Any, dtype[float32]]

Read cell (obs) embeddings and return as a dense numpy.ndarray. Any cells without an embedding will return NaN values.

@@ -245,7 +238,7 @@

cellxgene_census.experimental.get_embeddingnumpy.ndarray.

Raises:
-

ValueError – if the Census and embedding are mismatched.

+

ValueError – if the Census and embedding are mismatched.

Lifecycle

diff --git a/_autosummary/cellxgene_census.experimental.get_embedding_metadata.html b/_autosummary/cellxgene_census.experimental.get_embedding_metadata.html index 05eebac2e..8fc9311d0 100644 --- a/_autosummary/cellxgene_census.experimental.get_embedding_metadata.html +++ b/_autosummary/cellxgene_census.experimental.get_embedding_metadata.html @@ -123,13 +123,6 @@ - - -
- 1.16.2 -
- -
@@ -224,7 +217,7 @@

cellxgene_census.experimental.get_embedding_metadata

-cellxgene_census.experimental.get_embedding_metadata(embedding_uri: str, context: SOMATileDBContext | None = None) → dict[str, Any]
+cellxgene_census.experimental.get_embedding_metadata(embedding_uri: str, context: SOMATileDBContext | None = None) → dict[str, Any]

Read embedding metadata and return as a Python dict.

Parameters:
diff --git a/_autosummary/cellxgene_census.experimental.get_embedding_metadata_by_name.html b/_autosummary/cellxgene_census.experimental.get_embedding_metadata_by_name.html index a0b54ce02..4663a1634 100644 --- a/_autosummary/cellxgene_census.experimental.get_embedding_metadata_by_name.html +++ b/_autosummary/cellxgene_census.experimental.get_embedding_metadata_by_name.html @@ -123,13 +123,6 @@ - - -
- 1.16.2 -
- -
@@ -224,7 +217,7 @@

cellxgene_census.experimental.get_embedding_metadata_by_name

-cellxgene_census.experimental.get_embedding_metadata_by_name(embedding_name: str, organism: str, census_version: str, embedding_type: str | None = 'obs_embedding') → dict[str, Any]
+cellxgene_census.experimental.get_embedding_metadata_by_name(embedding_name: str, organism: str, census_version: str, embedding_type: str | None = 'obs_embedding') → dict[str, Any]

Return metadata for a specific embedding. If more embeddings match the query parameters, the most recent one will be returned.

@@ -240,7 +233,7 @@

cellxgene_census.experimental.get_embedding_metadata_by_name

A dictionary containing metadata describing the embedding.

Raises:
-

ValueError – if no embeddings are found for the specified query parameters.

+

ValueError – if no embeddings are found for the specified query parameters.

diff --git a/_autosummary/cellxgene_census.experimental.ml.encoders.BatchEncoder.html b/_autosummary/cellxgene_census.experimental.ml.encoders.BatchEncoder.html index c5afba03e..1fb98ad76 100644 --- a/_autosummary/cellxgene_census.experimental.ml.encoders.BatchEncoder.html +++ b/_autosummary/cellxgene_census.experimental.ml.encoders.BatchEncoder.html @@ -123,13 +123,6 @@ - - -
- 1.16.2 -
- -
@@ -227,11 +220,11 @@

cellxgene_census.experimental.ml.encoders.BatchEncoder

-class cellxgene_census.experimental.ml.encoders.BatchEncoder(cols: list[str], name: str = 'batch')
+class cellxgene_census.experimental.ml.encoders.BatchEncoder(cols: list[str], name: str = 'batch')

An encoder that concatenates and encodes several obs columns.

-__init__(cols: list[str], name: str = 'batch')
+__init__(cols: list[str], name: str = 'batch')

Methods

diff --git a/_autosummary/cellxgene_census.experimental.ml.encoders.Encoder.html b/_autosummary/cellxgene_census.experimental.ml.encoders.Encoder.html index faae340fa..2ea90d59f 100644 --- a/_autosummary/cellxgene_census.experimental.ml.encoders.Encoder.html +++ b/_autosummary/cellxgene_census.experimental.ml.encoders.Encoder.html @@ -123,13 +123,6 @@ - - -
- 1.16.2 -
- -
diff --git a/_autosummary/cellxgene_census.experimental.ml.encoders.LabelEncoder.html b/_autosummary/cellxgene_census.experimental.ml.encoders.LabelEncoder.html index c6876c436..d546015cd 100644 --- a/_autosummary/cellxgene_census.experimental.ml.encoders.LabelEncoder.html +++ b/_autosummary/cellxgene_census.experimental.ml.encoders.LabelEncoder.html @@ -123,13 +123,6 @@ - - -
- 1.16.2 -
- -
@@ -227,11 +220,11 @@

cellxgene_census.experimental.ml.encoders.LabelEncoder

-class cellxgene_census.experimental.ml.encoders.LabelEncoder(col: str)
+class cellxgene_census.experimental.ml.encoders.LabelEncoder(col: str)

Default encoder based on sklearn.preprocessing.LabelEncoder.

-__init__(col: str) → None
+__init__(col: str) → None

Methods

diff --git a/_autosummary/cellxgene_census.experimental.ml.huggingface.CellDatasetBuilder.html b/_autosummary/cellxgene_census.experimental.ml.huggingface.CellDatasetBuilder.html index bd6f355c9..f141c4eeb 100644 --- a/_autosummary/cellxgene_census.experimental.ml.huggingface.CellDatasetBuilder.html +++ b/_autosummary/cellxgene_census.experimental.ml.huggingface.CellDatasetBuilder.html @@ -123,13 +123,6 @@ - - -
- 1.16.2 -
- -
@@ -227,7 +220,7 @@

cellxgene_census.experimental.ml.huggingface.CellDatasetBuilder

-class cellxgene_census.experimental.ml.huggingface.CellDatasetBuilder(experiment: Experiment, measurement_name: str = 'RNA', layer_name: str = 'raw', *, block_size: int | None = None, **kwargs: Any)
+class cellxgene_census.experimental.ml.huggingface.CellDatasetBuilder(experiment: Experiment, measurement_name: str = 'RNA', layer_name: str = 'raw', *, block_size: int | None = None, **kwargs: Any)

Abstract base class for methods to process CELLxGENE Census ExperimentAxisQuery results into a Hugging Face Dataset in which each item represents one cell. Subclasses implement the cell_item() method to process each row of an X layer @@ -252,7 +245,7 @@

cellxgene_census.experimental.ml.huggingface.CellDatasetBuilder```

-__init__(experiment: Experiment, measurement_name: str = 'RNA', layer_name: str = 'raw', *, block_size: int | None = None, **kwargs: Any)
+__init__(experiment: Experiment, measurement_name: str = 'RNA', layer_name: str = 'raw', *, block_size: int | None = None, **kwargs: Any)

Initialize the CellDatasetBuilder to process the results of a Census ExperimentAxisQuery.

    diff --git a/_autosummary/cellxgene_census.experimental.ml.huggingface.GeneformerTokenizer.html b/_autosummary/cellxgene_census.experimental.ml.huggingface.GeneformerTokenizer.html index 2959149a4..0105f5525 100644 --- a/_autosummary/cellxgene_census.experimental.ml.huggingface.GeneformerTokenizer.html +++ b/_autosummary/cellxgene_census.experimental.ml.huggingface.GeneformerTokenizer.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -227,7 +220,7 @@

    cellxgene_census.experimental.ml.huggingface.GeneformerTokenizer

    -class cellxgene_census.experimental.ml.huggingface.GeneformerTokenizer(experiment: Experiment, *, obs_column_names: Sequence[str] | None = None, obs_attributes: Sequence[str] | None = None, max_input_tokens: int = 2048, special_token: bool = False, token_dictionary_file: str = '', gene_median_file: str = '', gene_mapping_file: str = '', **kwargs: Any)
    +class cellxgene_census.experimental.ml.huggingface.GeneformerTokenizer(experiment: Experiment, *, obs_column_names: Sequence[str] | None = None, obs_attributes: Sequence[str] | None = None, max_input_tokens: int = 2048, special_token: bool = False, token_dictionary_file: str = '', gene_median_file: str = '', gene_mapping_file: str = '', **kwargs: Any)

    Generate a Hugging Face Dataset containing Geneformer token sequences for each cell in CELLxGENE Census ExperimentAxisQuery results (human).

    This class requires the Geneformer package to be installed separately with: @@ -261,7 +254,7 @@

    cellxgene_census.experimental.ml.huggingface.GeneformerTokenizer
    -__init__(experiment: Experiment, *, obs_column_names: Sequence[str] | None = None, obs_attributes: Sequence[str] | None = None, max_input_tokens: int = 2048, special_token: bool = False, token_dictionary_file: str = '', gene_median_file: str = '', gene_mapping_file: str = '', **kwargs: Any) → None
    +__init__(experiment: Experiment, *, obs_column_names: Sequence[str] | None = None, obs_attributes: Sequence[str] | None = None, max_input_tokens: int = 2048, special_token: bool = False, token_dictionary_file: str = '', gene_median_file: str = '', gene_mapping_file: str = '', **kwargs: Any) → None

    Initialize GeneformerTokenizer.

    Args: - experiment: Census Experiment to query diff --git a/_autosummary/cellxgene_census.experimental.ml.pytorch.ExperimentDataPipe.html b/_autosummary/cellxgene_census.experimental.ml.pytorch.ExperimentDataPipe.html index a9512a15b..0579b7125 100644 --- a/_autosummary/cellxgene_census.experimental.ml.pytorch.ExperimentDataPipe.html +++ b/_autosummary/cellxgene_census.experimental.ml.pytorch.ExperimentDataPipe.html @@ -123,13 +123,6 @@ - - -

    - 1.16.2 -
    - -
    @@ -227,7 +220,7 @@

    cellxgene_census.experimental.ml.pytorch.ExperimentDataPipe

    -class cellxgene_census.experimental.ml.pytorch.ExperimentDataPipe(experiment: Experiment, measurement_name: str = 'RNA', X_name: str = 'raw', obs_query: AxisQuery | None = None, var_query: AxisQuery | None = None, obs_column_names: Sequence[str] = (), batch_size: int = 1, shuffle: bool = True, seed: int | None = None, return_sparse_X: bool = False, soma_chunk_size: int | None = 64, use_eager_fetch: bool = True, shuffle_chunk_count: int | None = 2000, encoders: list[cellxgene_census.experimental.ml.encoders.Encoder] | None = None)
    +class cellxgene_census.experimental.ml.pytorch.ExperimentDataPipe(experiment: Experiment, measurement_name: str = 'RNA', X_name: str = 'raw', obs_query: AxisQuery | None = None, var_query: AxisQuery | None = None, obs_column_names: Sequence[str] = (), batch_size: int = 1, shuffle: bool = True, seed: int | None = None, return_sparse_X: bool = False, soma_chunk_size: int | None = 64, use_eager_fetch: bool = True, shuffle_chunk_count: int | None = 2000, encoders: list[cellxgene_census.experimental.ml.encoders.Encoder] | None = None)

    An torchdata.datapipes.iter.IterDataPipe that reads obs and X data from a tiledbsoma.Experiment, based upon the specified queries along the obs and var axes. Provides an iterator over these data when the object is passed to Python’s built-in iter function.

    @@ -263,7 +256,7 @@

    cellxgene_census.experimental.ml.pytorch.ExperimentDataPipe
    -__init__(experiment: Experiment, measurement_name: str = 'RNA', X_name: str = 'raw', obs_query: AxisQuery | None = None, var_query: AxisQuery | None = None, obs_column_names: Sequence[str] = (), batch_size: int = 1, shuffle: bool = True, seed: int | None = None, return_sparse_X: bool = False, soma_chunk_size: int | None = 64, use_eager_fetch: bool = True, shuffle_chunk_count: int | None = 2000, encoders: list[cellxgene_census.experimental.ml.encoders.Encoder] | None = None) → None
    +__init__(experiment: Experiment, measurement_name: str = 'RNA', X_name: str = 'raw', obs_query: AxisQuery | None = None, var_query: AxisQuery | None = None, obs_column_names: Sequence[str] = (), batch_size: int = 1, shuffle: bool = True, seed: int | None = None, return_sparse_X: bool = False, soma_chunk_size: int | None = 64, use_eager_fetch: bool = True, shuffle_chunk_count: int | None = 2000, encoders: list[cellxgene_census.experimental.ml.encoders.Encoder] | None = None) → None

    Construct a new ExperimentDataPipe.

    Parameters:
    diff --git a/_autosummary/cellxgene_census.experimental.ml.pytorch.Stats.html b/_autosummary/cellxgene_census.experimental.ml.pytorch.Stats.html index 6195605f1..c699de7fc 100644 --- a/_autosummary/cellxgene_census.experimental.ml.pytorch.Stats.html +++ b/_autosummary/cellxgene_census.experimental.ml.pytorch.Stats.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -227,14 +220,14 @@

    cellxgene_census.experimental.ml.pytorch.Stats

    -class cellxgene_census.experimental.ml.pytorch.Stats(n_obs: int = 0, nnz: int = 0, elapsed: float = 0, n_soma_chunks: int = 0)
    +class cellxgene_census.experimental.ml.pytorch.Stats(n_obs: int = 0, nnz: int = 0, elapsed: float = 0, n_soma_chunks: int = 0)

    Statistics about the data retrieved by ExperimentDataPipe via SOMA API. This is useful for assessing the read throughput of SOMA data.

    Lifecycle

    experimental

    -__init__(n_obs: int = 0, nnz: int = 0, elapsed: float = 0, n_soma_chunks: int = 0) → None
    +__init__(n_obs: int = 0, nnz: int = 0, elapsed: float = 0, n_soma_chunks: int = 0) → None

    Method generated by attrs for class Stats.

    diff --git a/_autosummary/cellxgene_census.experimental.ml.pytorch.experiment_dataloader.html b/_autosummary/cellxgene_census.experimental.ml.pytorch.experiment_dataloader.html index 377c16730..f9d1d5cbc 100644 --- a/_autosummary/cellxgene_census.experimental.ml.pytorch.experiment_dataloader.html +++ b/_autosummary/cellxgene_census.experimental.ml.pytorch.experiment_dataloader.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -227,7 +220,7 @@

    cellxgene_census.experimental.ml.pytorch.experiment_dataloader

    -cellxgene_census.experimental.ml.pytorch.experiment_dataloader(datapipe: IterDataPipe, num_workers: int = 0, **dataloader_kwargs: Any) → DataLoader
    +cellxgene_census.experimental.ml.pytorch.experiment_dataloader(datapipe: IterDataPipe, num_workers: int = 0, **dataloader_kwargs: Any) → DataLoader

    Factory method for torch.utils.data.DataLoader. This method can be used to safely instantiate a torch.utils.data.DataLoader that works with cellxgene_census.experimental.ml.pytorch.ExperimentDataPipe, since some of the torch.utils.data.DataLoader constructor parameters are not applicable when using a @@ -250,7 +243,7 @@

    cellxgene_census.experimental.ml.pytorch.experiment_dataloader

    A torch.utils.data.DataLoader.

    Raises:
    -

    ValueError – if any of the shuffle, batch_size, sampler, batch_sampler, or collate_fn params +

    ValueError – if any of the shuffle, batch_size, sampler, batch_sampler, or collate_fn params are passed as keyword arguments.

    diff --git a/_autosummary/cellxgene_census.experimental.pp.get_highly_variable_genes.html b/_autosummary/cellxgene_census.experimental.pp.get_highly_variable_genes.html index a3b4a143c..96758dd26 100644 --- a/_autosummary/cellxgene_census.experimental.pp.get_highly_variable_genes.html +++ b/_autosummary/cellxgene_census.experimental.pp.get_highly_variable_genes.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -222,7 +215,7 @@

    cellxgene_census.experimental.pp.get_highly_variable_genes

    -cellxgene_census.experimental.pp.get_highly_variable_genes(census: Collection, organism: str, measurement_name: str = 'RNA', X_name: str = 'raw', obs_value_filter: str | None = None, obs_coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = None, var_value_filter: str | None = None, var_coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = None, n_top_genes: int = 1000, flavor: Literal['seurat_v3'] = 'seurat_v3', span: float = 0.3, batch_key: str | Sequence[str] | None = None, max_loess_jitter: float = 1e-06, batch_key_func: Callable[[...], Any] | None = None) → DataFrame
    +cellxgene_census.experimental.pp.get_highly_variable_genes(census: Collection, organism: str, measurement_name: str = 'RNA', X_name: str = 'raw', obs_value_filter: str | None = None, obs_coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = None, var_value_filter: str | None = None, var_coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = None, n_top_genes: int = 1000, flavor: Literal['seurat_v3'] = 'seurat_v3', span: float = 0.3, batch_key: str | Sequence[str] | None = None, max_loess_jitter: float = 1e-06, batch_key_func: Callable[[...], Any] | None = None) → DataFrame

    Convience wrapper around tiledbsoma.Experiment query and cellxgene_census.experimental.pp.highly_variable_genes() function, to build and execute a query, and annotate the query result genes (var dataframe) based upon variability.

    @@ -258,7 +251,7 @@

    cellxgene_census.experimental.pp.get_highly_variable_genes

    pandas.DataFrame containing annotations for all var values specified by the query.

    Raises:
    -

    ValueError – if the flavor paramater is not "seurat_v3".

    +

    ValueError – if the flavor paramater is not "seurat_v3".

    diff --git a/_autosummary/cellxgene_census.experimental.pp.highly_variable_genes.html b/_autosummary/cellxgene_census.experimental.pp.highly_variable_genes.html index f252e7e9b..6b7fd00bf 100644 --- a/_autosummary/cellxgene_census.experimental.pp.highly_variable_genes.html +++ b/_autosummary/cellxgene_census.experimental.pp.highly_variable_genes.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -222,7 +215,7 @@

    cellxgene_census.experimental.pp.highly_variable_genes

    -cellxgene_census.experimental.pp.highly_variable_genes(query: ExperimentAxisQuery, n_top_genes: int = 1000, layer: str = 'raw', flavor: Literal['seurat_v3'] = 'seurat_v3', span: float = 0.3, batch_key: str | Sequence[str] | None = None, max_loess_jitter: float = 1e-06, batch_key_func: Callable[[...], Any] | None = None) → DataFrame
    +cellxgene_census.experimental.pp.highly_variable_genes(query: ExperimentAxisQuery, n_top_genes: int = 1000, layer: str = 'raw', flavor: Literal['seurat_v3'] = 'seurat_v3', span: float = 0.3, batch_key: str | Sequence[str] | None = None, max_loess_jitter: float = 1e-06, batch_key_func: Callable[[...], Any] | None = None) → DataFrame

    Identify and annotate highly variable genes contained in the query results. The API is modelled on ScanPy scanpy.pp.highly_variable_genes API. Results returned will mimic ScanPy results. The only flavor available @@ -254,7 +247,7 @@

    cellxgene_census.experimental.pp.highly_variable_genesscanpy.pp.highly_variable_genes().

    Raises:
    -

    ValueError – if the flavor parameter is not "seurat_v3".

    +

    ValueError – if the flavor parameter is not "seurat_v3".

    Examples

    diff --git a/_autosummary/cellxgene_census.experimental.pp.mean_variance.html b/_autosummary/cellxgene_census.experimental.pp.mean_variance.html index c2dfa21f3..a1b1b9e6e 100644 --- a/_autosummary/cellxgene_census.experimental.pp.mean_variance.html +++ b/_autosummary/cellxgene_census.experimental.pp.mean_variance.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -222,7 +215,7 @@

    cellxgene_census.experimental.pp.mean_variance

    -cellxgene_census.experimental.pp.mean_variance(query: ExperimentAxisQuery, layer: str = 'raw', axis: int = 0, calculate_mean: bool = False, calculate_variance: bool = False, ddof: int = 1, nnz_only: bool = False) → DataFrame
    +cellxgene_census.experimental.pp.mean_variance(query: ExperimentAxisQuery, layer: str = 'raw', axis: int = 0, calculate_mean: bool = False, calculate_variance: bool = False, ddof: int = 1, nnz_only: bool = False) → DataFrame

    Calculate mean and/or variance along the obs axis from query results. Calculations are done in an accumulative chunked fashion. For the mean and variance calculations, the total number of elements (N) is, by default, the corresponding dimension size: for column-wise calculations (axis = 0) N is number of rows, for row-wise diff --git a/_autosummary/cellxgene_census.get_anndata.html b/_autosummary/cellxgene_census.get_anndata.html index 357956037..2b446e9c8 100644 --- a/_autosummary/cellxgene_census.get_anndata.html +++ b/_autosummary/cellxgene_census.get_anndata.html @@ -123,13 +123,6 @@ - - -

    - 1.16.2 -
    - -
    @@ -222,7 +215,7 @@

    cellxgene_census.get_anndata

    -cellxgene_census.get_anndata(census: Collection, organism: str, measurement_name: str = 'RNA', X_name: str = 'raw', X_layers: Sequence[str] | None = (), obsm_layers: Sequence[str] | None = (), obsp_layers: Sequence[str] | None = (), varm_layers: Sequence[str] | None = (), varp_layers: Sequence[str] | None = (), obs_value_filter: str | None = None, obs_coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = None, var_value_filter: str | None = None, var_coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = None, column_names: AxisColumnNames | None = None, obs_embeddings: Sequence[str] | None = (), var_embeddings: Sequence[str] | None = (), obs_column_names: Sequence[str] | None = None, var_column_names: Sequence[str] | None = None) → AnnData
    +cellxgene_census.get_anndata(census: Collection, organism: str, measurement_name: str = 'RNA', X_name: str = 'raw', X_layers: Sequence[str] | None = (), obsm_layers: Sequence[str] | None = (), obsp_layers: Sequence[str] | None = (), varm_layers: Sequence[str] | None = (), varp_layers: Sequence[str] | None = (), obs_value_filter: str | None = None, obs_coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = None, var_value_filter: str | None = None, var_coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = None, column_names: AxisColumnNames | None = None, obs_embeddings: Sequence[str] | None = (), var_embeddings: Sequence[str] | None = (), obs_column_names: Sequence[str] | None = None, var_column_names: Sequence[str] | None = None) → AnnData

    Convenience wrapper around tiledbsoma.Experiment query, to build and execute a query, and return it as an anndata.AnnData object.

    diff --git a/_autosummary/cellxgene_census.get_census_version_description.html b/_autosummary/cellxgene_census.get_census_version_description.html index 07fd67da3..22d3176e1 100644 --- a/_autosummary/cellxgene_census.get_census_version_description.html +++ b/_autosummary/cellxgene_census.get_census_version_description.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -221,7 +214,7 @@

    cellxgene_census.get_census_version_description

    -cellxgene_census.get_census_version_description(census_version: str) → CensusVersionDescription
    +cellxgene_census.get_census_version_description(census_version: str) → CensusVersionDescription

    Get release description for given Census version, from the Census release directory.

    Parameters:
    @@ -231,7 +224,7 @@

    cellxgene_census.get_census_version_description

    CensusVersionDescription - a dictionary containing a description of the release.

    Raises:
    -

    ValueError – if unknown census_version value.

    +

    ValueError – if unknown census_version value.

    Lifecycle

    diff --git a/_autosummary/cellxgene_census.get_census_version_directory.html b/_autosummary/cellxgene_census.get_census_version_directory.html index cd36f6708..89aa9cb66 100644 --- a/_autosummary/cellxgene_census.get_census_version_directory.html +++ b/_autosummary/cellxgene_census.get_census_version_directory.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -221,7 +214,7 @@

    cellxgene_census.get_census_version_directory

    -cellxgene_census.get_census_version_directory(*, lts: bool | None = None, retracted: bool | None = False) → dict[str, cellxgene_census._release_directory.CensusVersionDescription]
    +cellxgene_census.get_census_version_directory(*, lts: bool | None = None, retracted: bool | None = False) → dict[str, cellxgene_census._release_directory.CensusVersionDescription]

    Get the directory of Census versions currently available, optionally filtering by specified flags. If a filtering flag is not specified, Census versions will not be filtered by that flag. Defaults to including both “long-term stable” (LTS) and weekly Census versions, and excluding diff --git a/_autosummary/cellxgene_census.get_default_soma_context.html b/_autosummary/cellxgene_census.get_default_soma_context.html index 1210790a2..7d8d24912 100644 --- a/_autosummary/cellxgene_census.get_default_soma_context.html +++ b/_autosummary/cellxgene_census.get_default_soma_context.html @@ -123,13 +123,6 @@ - - -

    - 1.16.2 -
    - -
    @@ -223,7 +216,7 @@

    cellxgene_census.get_default_soma_context

    -cellxgene_census.get_default_soma_context(tiledb_config: dict[str, Any] | None = None) → SOMATileDBContext
    +cellxgene_census.get_default_soma_context(tiledb_config: dict[str, Any] | None = None) → SOMATileDBContext

    Return a tiledbsoma.SOMATileDBContext with sensible defaults that can be further customized by the user. The customized context can then be passed to cellxgene_census.open_soma() with the context argument or to somacore.SOMAObject.open() with the context argument, such as diff --git a/_autosummary/cellxgene_census.get_obs.html b/_autosummary/cellxgene_census.get_obs.html index c795a946b..dfadb5dc9 100644 --- a/_autosummary/cellxgene_census.get_obs.html +++ b/_autosummary/cellxgene_census.get_obs.html @@ -123,13 +123,6 @@ - - -

    - 1.16.2 -
    - -
    @@ -222,7 +215,7 @@

    cellxgene_census.get_obs

    -cellxgene_census.get_obs(census: Collection, organism: str, *, value_filter: str | None = None, coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = slice(None, None, None), column_names: Sequence[str] | None = None) → DataFrame
    +cellxgene_census.get_obs(census: Collection, organism: str, *, value_filter: str | None = None, coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = slice(None, None, None), column_names: Sequence[str] | None = None) → DataFrame

    Get the observation metadata for a query on the census.

    Parameters:
    diff --git a/_autosummary/cellxgene_census.get_presence_matrix.html b/_autosummary/cellxgene_census.get_presence_matrix.html index f6fe679b9..4c5626290 100644 --- a/_autosummary/cellxgene_census.get_presence_matrix.html +++ b/_autosummary/cellxgene_census.get_presence_matrix.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -220,7 +213,7 @@

    cellxgene_census.get_presence_matrix

    -cellxgene_census.get_presence_matrix(census: Collection, organism: str, measurement_name: str = 'RNA') → csr_matrix
    +cellxgene_census.get_presence_matrix(census: Collection, organism: str, measurement_name: str = 'RNA') → csr_matrix

    Read the feature dataset presence matrix and return as a scipy.sparse.csr_array. The returned sparse matrix is indexed on the first dimension by the dataset soma_joinid values, and on the second dimension by the var pandas.DataFrame soma_joinid values.

    @@ -236,7 +229,7 @@

    cellxgene_census.get_presence_matrix

    A scipy.sparse.csr_array object containing the presence matrix.

    Raises:
    -

    ValueError – if the organism cannot be found.

    +

    ValueError – if the organism cannot be found.

    Lifecycle

    diff --git a/_autosummary/cellxgene_census.get_source_h5ad_uri.html b/_autosummary/cellxgene_census.get_source_h5ad_uri.html index f8e25772c..7467af360 100644 --- a/_autosummary/cellxgene_census.get_source_h5ad_uri.html +++ b/_autosummary/cellxgene_census.get_source_h5ad_uri.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -223,7 +216,7 @@

    cellxgene_census.get_source_h5ad_uri

    -cellxgene_census.get_source_h5ad_uri(dataset_id: str, *, census_version: str = 'stable') → CensusLocator
    +cellxgene_census.get_source_h5ad_uri(dataset_id: str, *, census_version: str = 'stable') → CensusLocator

    Open the named version of the census, and return the URI for the dataset_id. This does not guarantee that the H5AD exists or is accessible to the user.

    @@ -238,7 +231,7 @@

    cellxgene_census.get_source_h5ad_uriRaises: -

    KeyError – if either dataset_id or census_version do not exist.

    +

    KeyError – if either dataset_id or census_version do not exist.

    Lifecycle

    diff --git a/_autosummary/cellxgene_census.get_var.html b/_autosummary/cellxgene_census.get_var.html index 00322d525..b457b9377 100644 --- a/_autosummary/cellxgene_census.get_var.html +++ b/_autosummary/cellxgene_census.get_var.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -222,7 +215,7 @@

    cellxgene_census.get_var

    -cellxgene_census.get_var(census: Collection, organism: str, *, value_filter: str | None = None, coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = slice(None, None, None), column_names: Sequence[str] | None = None) → DataFrame
    +cellxgene_census.get_var(census: Collection, organism: str, *, value_filter: str | None = None, coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = slice(None, None, None), column_names: Sequence[str] | None = None) → DataFrame

    Get the variable metadata for a query on the census.

    Parameters:
    diff --git a/_autosummary/cellxgene_census.open_soma.html b/_autosummary/cellxgene_census.open_soma.html index d41718b04..73882d018 100644 --- a/_autosummary/cellxgene_census.open_soma.html +++ b/_autosummary/cellxgene_census.open_soma.html @@ -123,13 +123,6 @@ - - -
    - 1.16.2 -
    - -
    @@ -223,7 +216,7 @@

    cellxgene_census.open_soma

    -cellxgene_census.open_soma(*, census_version: str | None = 'stable', mirror: str | None = None, uri: str | None = None, tiledb_config: dict[str, Any] | None = None, context: SOMATileDBContext | None = None) → Collection
    +cellxgene_census.open_soma(*, census_version: str | None = 'stable', mirror: str | None = None, uri: str | None = None, tiledb_config: dict[str, Any] | None = None, context: SOMATileDBContext | None = None) → Collection

    Open the Census by version or URI.

    Parameters:
    @@ -246,7 +239,7 @@

    cellxgene_census.open_somaRaises: -

    ValueError – if the census cannot be found, the URI cannot be opened, neither a URI +

    ValueError – if the census cannot be found, the URI cannot be opened, neither a URI or a version are specified, or an invalid mirror is provided.

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    + ${config.projects.translations + .map( + (translation) => ` +
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    +
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    + +
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    +
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