# API

```{eval-rst}
.. module:: anndata
```

The central class:

```{eval-rst}
.. autosummary::
   :toctree: generated/

   AnnData
```

Its attributes are reflected in the {doc}`/accessors` API ({mod}`!anndata.acc`).
If you want to write e.g. plotting or validation code for anndata objects, look there!

```{eval-rst}
.. toctree::
   :hidden:

   anndata.acc <accessors>
```

(combining-api)=

## Combining

Combining {class}`AnnData` objects.
See also the section on concatenation.

```{eval-rst}
.. autosummary::
   :toctree: generated/

   concat
```

(reading-api)=

## Reading

Reading anndata’s native formats `.h5ad` and `zarr`.

```{eval-rst}
.. autosummary::
   :toctree: generated/

   io.read_h5ad
   io.read_zarr
```

Reading individual portions ({attr}`~AnnData.obs`, {attr}`~AnnData.varm` etc.) of the {class}`AnnData` object.

```{eval-rst}
.. autosummary::
   :toctree: generated/

   io.read_elem
   io.sparse_dataset
```

Reading file formats that cannot represent all aspects of {class}`AnnData` objects.

```{tip}
You might have more success by assembling the {class}`AnnData` object yourself from the individual parts.
```

```{eval-rst}
.. autosummary::
   :toctree: generated/

   io.read_csv
   io.read_excel
   io.read_hdf
   io.read_mtx
   io.read_text
   io.read_umi_tools
```

(writing-api)=

## Writing

Writing a complete {class}`AnnData` object to disk in anndata’s native formats `.h5ad` and `zarr`.
(These functions are also exported as {func}`io.write_h5ad` and {func}`io.write_zarr`.)

```{eval-rst}
.. autosummary::
   :toctree: generated/

   AnnData.write_h5ad
   AnnData.write_zarr
   AnnData.unwriteable


..
    .. autosummary::
       :toctree: generated/

       io.read_loom
       AnnData.write_loom
       io.write_h5ad
       io.write_zarr

.. toctree::
   :hidden:

   generated/anndata.io.read_loom
   generated/anndata.AnnData.write_loom
   generated/anndata.io.write_h5ad
   generated/anndata.io.write_zarr
```

Writing individual portions ({attr}`~AnnData.obs`, {attr}`~AnnData.varm` etc.) of the {class}`AnnData` object.

```{eval-rst}
.. autosummary::
   :toctree: generated/

   io.write_elem
```

Writing formats that cannot represent all aspects of {class}`AnnData` objects.

```{eval-rst}
.. autosummary::
   :toctree: generated/

   AnnData.write_csvs
```

(experimental-api)=

## Experimental API

```{warning}
APIs in the experimental module are currently in development and subject to change at any time.
```

Two classes for working with batched access to collections of many {class}`AnnData` objects or `.h5ad` files.
In particular, for pytorch-based models.

```{eval-rst}
.. autosummary::
   :toctree: generated/

   experimental.AnnCollection
   experimental.AnnLoader
```

:::{class} experimental.AnnCollectionView

A view of {class}`experimental.AnnCollection` with most of the same functions and attributes.
:::

```{note}
`AnnLoader` is deprecated and will be removed in 0.14.
Please see {class}`annbatch.Loader` for the replacement.
```

Out of core concatenation

```{eval-rst}
.. autosummary::
   :toctree: generated/

   experimental.concat_on_disk
```

Low level methods for reading and writing elements of an {class}`AnnData` object to a store:

```{eval-rst}
.. autosummary::
   :toctree: generated/

   experimental.read_elem_lazy
   experimental.read_lazy
```

Utilities for customizing the IO process:

```{eval-rst}
.. autosummary::
   :toctree: generated/

   experimental.read_dispatched
   experimental.write_dispatched
```

Types used by the former:

```{eval-rst}
.. autosummary::
   :toctree: generated/
   :template: class-minimal
   :signatures: none

   experimental.IOSpec
   experimental.Read
   experimental.Write
   experimental.ReadCallback
   experimental.WriteCallback
   experimental.backed.MaskedArray
   experimental.backed.CategoricalArray
   experimental.backed.Dataset2D
   experimental.Dataset2DIlocIndexer

..
    this is not a class/protocol so since the above
    specifies a template, it gets used.

.. autosummary::
   :toctree: generated/

   experimental.StorageType
```

(extensions-api)=

## Extensions

```{eval-rst}
.. autosummary::
   :toctree: generated/

   register_anndata_namespace

```

Types used by the former:

```{eval-rst}
.. autosummary::
   :toctree: generated/

   types.SupportsArrayApiBase
   types.SupportsArrayApi

.. toctree::
   :hidden:

   generated/anndata.types.ExtensionNamespace
```

{class}`scverse_misc.ExtensionNamespace`

(errors-api)=

## Errors and warnings

```{eval-rst}
.. autosummary::
   :toctree: generated/

   ImplicitModificationWarning
```

(settings-api)=

## Settings

```{eval-rst}
.. autosummary::
   :toctree: generated/

   settings
   settings.override
   settings.reset
```

(types-api)=

## Custom Types/Classes for Readable/Writeable Elements

```{eval-rst}
.. autosummary::
   :toctree: generated/
   :template: class-minimal

   abc.CSRDataset
   abc.CSCDataset
```

<!-- these are types, not classes, so don’t use the above template -->

```{eval-rst}
.. toctree::
   :hidden:

   typing

.. autosummary::

   typing.Index1D
   typing.Index
   typing.InMemoryArray
   typing.AlignedArray
   typing.Storable
   typing.RWAble
```