annsel.AnnselAccessor.filter

annsel.AnnselAccessor.filter#

AnnselAccessor.filter(self, obs=None, var=None, x=None, obs_names=None, var_names=None, obsm=None, varm=None, layer=None, copy=False)[source]#

Filter the AnnData object by the given predicates.

Parameters:
obs Expr | str | Series | Iterable[Expr | str | Series] | None (default: None)

Predicates to filter the observations by.

var Expr | str | Series | Iterable[Expr | str | Series] | None (default: None)

Predicates to filter the variables by.

x Expr | str | Series | Iterable[Expr | str | Series] | None (default: None)

Predicates to filter the data by.

obs_names Expr | str | Series | Iterable[Expr | str | Series] | None (default: None)

Predicates to filter the observation names by.

var_names Expr | str | Series | Iterable[Expr | str | Series] | None (default: None)

Predicates to filter the variable names by.

obsm Mapping[str, Expr | str | Series | Iterable[Expr | str | Series]] | None (default: None)

A mapping of obsm keys and predicates to filter the obsm matrices by.

varm Mapping[str, Expr | str | Series | Iterable[Expr | str | Series]] | None (default: None)

A mapping of varm keys and predicates to filter the varm matrices by.

layer str | None (default: None)

The layer to filter.

copy bool (default: False)

Whether to return a copy of the AnnData object.

Return type:

AnnData

Returns:

The filtered AnnData object.

Examples

>>> import annsel as an
>>> adata = an.datasets.leukemic_bone_marrow_dataset()
>>> adata.an.filter(
...     obs=(
...         an.col(["Cell_label"]).is_in(["Classical Monocytes", "CD8+CD103+ tissue resident memory T cells"]),
...         an.col(["sex"]) == "male",
...     ),
...     var=an.col(["vst.mean"]) >= 3,
... )
AnnData object with n_obs × n_vars = 6741 × 458
     obs: 'Cluster_ID', 'donor_id', 'Sample_Tag', 'Cell_label', 'is_primary_data', 'organism_ontology_term_id', 'self_reported_ethnicity_ontology_term_id', 'assay_ontology_term_id', 'tissue_ontology_term_id', 'Genotype', 'development_stage_ontology_term_id', 'sex_ontology_term_id', 'disease_ontology_term_id', 'cell_type_ontology_term_id', 'suspension_type', 'tissue_type', 'cell_type', 'assay', 'disease', 'organism', 'sex', 'tissue', 'self_reported_ethnicity', 'development_stage', 'observation_joinid'
     var: 'vst.mean', 'vst.variance', 'vst.variance.expected', 'vst.variance.standardized', 'vst.variable', 'feature_is_filtered', 'Unnamed: 0', 'feature_name', 'feature_reference', 'feature_biotype', 'feature_length', 'feature_type'
     uns: 'cell_type_ontology_term_id_colors', 'citation', 'default_embedding', 'schema_reference', 'schema_version', 'title'
     obsm: 'X_bothumap', 'X_pca', 'X_projected', 'X_projectedmean', 'X_tsneni', 'X_umapni'
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