The tiledbsoma.io module¶

Functions¶

Data conversion to/from TileDB-SOMA

`tiledbsoma.io.from_h5ad`	Reads an `.h5ad` file and writes it to an `Experiment`.
`tiledbsoma.io.from_anndata`	Writes an AnnData object to an `Experiment`.
`tiledbsoma.io.to_h5ad`	Converts the experiment group to AnnData format and writes it to the specified `.h5ad` file.
`tiledbsoma.io.to_anndata`	Converts the experiment group to AnnData format.

Updating values within a TileDB-SOMA Experiment

`tiledbsoma.io.add_X_layer`	This is useful for adding X data, for example from Scanpy's `scanpy.pp.normalize_total`, `scanpy.pp.log1p`, etc.
`tiledbsoma.io.add_matrix_to_collection`	This is useful for adding X/obsp/varm/etc data, for example from Scanpy's `scanpy.pp.normalize_total`, `scanpy.pp.log1p`, etc.
`tiledbsoma.io.create_from_matrix`	Create and populate the `soma_matrix` from the contents of `matrix`.
`tiledbsoma.io.update_obs`	Given a new Pandas dataframe with desired contents, updates the SOMA experiment's entire `obs` to incorporate the changes.
`tiledbsoma.io.update_var`	Given a new Pandas dataframe with desired contents, updates the SOMA experiment's specified measurement's entire `var` to incorporate the changes.
`tiledbsoma.io.update_matrix`	Given a `SparseNDArray` or `DenseNDArray` already opened for write, writes the new data.

Growing a TileDB-SOMA Experiment

`tiledbsoma.io.register_anndatas`	Extends registration data from the baseline, already-written SOMA experiment to include multiple H5AD input files.
`tiledbsoma.io.register_h5ads`	Extends registration data from the baseline, already-written SOMA experiment to include multiple H5AD input files.
`tiledbsoma.io.append_X`	Appends new data to an existing `X` matrix.
`tiledbsoma.io.append_obs`	Writes new rows to an existing `obs` dataframe.
`tiledbsoma.io.append_var`	Writes new rows to an existing `var` dataframe.
`tiledbsoma.io.show_experiment_shapes`	For each dataframe/array contained within the SOMA `Experiment` pointed to by the given URI, shows the `non_empty_domain` (for dataframes), along with the `shape` and `maxshape` (for arrays) or `domain` and `maxdomain` (for dataframes).
`tiledbsoma.io.upgrade_experiment_shapes`	For each dataframe contained within the SOMA `Experiment` pointed to by the given URI, sets the `domain` to match the dataframe's current `non_empty_domain`.
`tiledbsoma.io.resize_experiment`	For each dataframe contained within the SOMA `Experiment` pointed to by the given URI, resizes the `domain` for the `soma_joinid` index column (if it is an indexed column) to match the desired new value.