# anndata for R

> **⚠️ This package is superseded by
> [anndataR](https://anndataR.scverse.org).**
>
> `anndataR` provides a pure R implementation of the `AnnData` data
> structure with no Python required. It reads and writes `.h5ad` files
> natively and supports conversion to/from `SingleCellExperiment` and
> `Seurat` objects. New users should install `anndataR` from
> Bioconductor instead:
>
> ``` r
> BiocManager::install("anndataR")
> ```
>
> Existing users of `anndata` can follow the [migration
> guide](https://anndata.dynverse.org/articles/migration_to_anndataR.html)
> for guidance on switching to `anndataR`.

`anndata` for R is a `reticulate` wrapper for the Python `anndata`
package.

## Installation

> **Note:** New projects should use
> [anndataR](https://anndataR.scverse.org) instead. See the [migration
> guide](https://anndata.dynverse.org/articles/migration_to_anndataR.html).

You can install `anndata` for R from CRAN as follows:

``` r
install.packages("anndata")
```

Normally, reticulate should take care of installing Miniconda and the
Python anndata.

If not, try running:

``` r
reticulate::install_miniconda()
anndata::install_anndata()
```

## Getting started

The API of anndata for R is very similar to its Python counterpart. Here
is an example:

``` r
library(anndata)

ad <- read_h5ad("example_formats/pbmc_1k_protein_v3_processed.h5ad")

ad
```

``` R
## AnnData object with n_obs × n_vars = 713 × 33538
##     var: 'gene_ids', 'feature_types', 'genome', 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
##     uns: 'hvgParameters', 'normalizationParameters', 'pca', 'pcaParameters'
##     obsm: 'X_pca'
##     varm: 'PCs'
```

``` r
Matrix::rowMeans(ad$X[1:10, ])
```

``` R
## AAACCCAAGTGGTCAG-1 AAAGGTATCAACTACG-1 AAAGTCCAGCGTGTCC-1 AACACACTCAAGAGTA-1 
##         0.06499579         0.06385104         0.06102355         0.06739055 
## AACACACTCGACGAGA-1 AACAGGGCAGGAGGTT-1 AACAGGGCAGTGTATC-1 AACAGGGTCAGAATAG-1 
##         0.08891241         0.08648681         0.09318970         0.09140243 
## AACCTGAAGATGGTCG-1 AACGGGATCGTTATCT-1 
##         0.06664118         0.07866523
```

See
[`?anndata`](https://anndata.dynverse.org/reference/anndata-package.md)
for a full list of the functions provided by this package. Check out any
of the other vignettes by clicking any of the links below:

- [Getting
  started](https://anndata.dynverse.org/articles/getting_started.html)
- [Migrating from anndata to
  anndataR](https://anndata.dynverse.org/articles/migration_to_anndataR.html)
- [Demo with
  scanpy](https://anndata.dynverse.org/articles/scanpy_demo.html)

## Future work

This package is no longer under active development as it has been
superseded by [anndataR](https://anndataR.scverse.org). Bug fixes may
still be applied, but no new features are planned.

## References

# Package index

## Package documentation

- [`anndata-package`](https://anndata.dynverse.org/reference/anndata-package.md)
  [`anndata`](https://anndata.dynverse.org/reference/anndata-package.md)
  **\[superseded\]** : anndata - Annotated Data

## Creating an AnnData object

- [`AnnData()`](https://anndata.dynverse.org/reference/AnnData.md) :
  Create an Annotated Data Matrix

## Concatenating two or more AnnData objects

- [`concat()`](https://anndata.dynverse.org/reference/concat.md)
  **\[superseded\]** : concat

## Reading an AnnData object from a file

- [`read_csv()`](https://anndata.dynverse.org/reference/read_csv.md)
  **\[superseded\]** : read_csv
- [`read_excel()`](https://anndata.dynverse.org/reference/read_excel.md)
  **\[superseded\]** : read_excel
- [`read_h5ad()`](https://anndata.dynverse.org/reference/read_h5ad.md)
  **\[superseded\]** : read_h5ad
- [`read_hdf()`](https://anndata.dynverse.org/reference/read_hdf.md)
  **\[superseded\]** : read_hdf
- [`read_loom()`](https://anndata.dynverse.org/reference/read_loom.md)
  **\[superseded\]** : read_loom
- [`read_mtx()`](https://anndata.dynverse.org/reference/read_mtx.md)
  **\[superseded\]** : read_mtx
- [`read_text()`](https://anndata.dynverse.org/reference/read_text.md)
  **\[superseded\]** : read_text
- [`read_umi_tools()`](https://anndata.dynverse.org/reference/read_umi_tools.md)
  **\[superseded\]** : read_umi_tools
- [`read_zarr()`](https://anndata.dynverse.org/reference/read_zarr.md)
  **\[superseded\]** : Read from a hierarchical Zarr array store.

## Writing an AnnData object to a file

- [`write_csvs()`](https://anndata.dynverse.org/reference/write_csvs.md)
  **\[superseded\]** : Write annotation to .csv files.
- [`write_h5ad()`](https://anndata.dynverse.org/reference/write_h5ad.md)
  **\[superseded\]** : Write .h5ad-formatted hdf5 file.
- [`write_loom()`](https://anndata.dynverse.org/reference/write_loom.md)
  **\[superseded\]** : Write .loom-formatted hdf5 file.
- [`write_zarr()`](https://anndata.dynverse.org/reference/write_zarr.md)
  **\[superseded\]** : Write a hierarchical Zarr array store.

## Installer

Helper function for installing the anndata Python package

- [`install_anndata()`](https://anndata.dynverse.org/reference/install_anndata.md)
  **\[deprecated\]** : Install anndata

## Helper functions / sugar syntax

- [`Layers()`](https://anndata.dynverse.org/reference/Layers.md) :
  Create a Layers object
- [`Raw()`](https://anndata.dynverse.org/reference/Raw.md) : Create a
  Raw object
- [`dimnames(`*`<AnnDataR6>`*`)`](https://anndata.dynverse.org/reference/AnnDataHelpers.md)
  [`` `dimnames<-`( ``*`<AnnDataR6>`*`)`](https://anndata.dynverse.org/reference/AnnDataHelpers.md)
  [`dim(`*`<AnnDataR6>`*`)`](https://anndata.dynverse.org/reference/AnnDataHelpers.md)
  [`as.data.frame(`*`<AnnDataR6>`*`)`](https://anndata.dynverse.org/reference/AnnDataHelpers.md)
  [`as.matrix(`*`<AnnDataR6>`*`)`](https://anndata.dynverse.org/reference/AnnDataHelpers.md)
  [`r_to_py(`*`<AnnDataR6>`*`)`](https://anndata.dynverse.org/reference/AnnDataHelpers.md)
  [`py_to_r(`*`<anndata._core.anndata.AnnData>`*`)`](https://anndata.dynverse.org/reference/AnnDataHelpers.md)
  [`` `[`( ``*`<AnnDataR6>`*`)`](https://anndata.dynverse.org/reference/AnnDataHelpers.md)
  [`t(`*`<AnnDataR6>`*`)`](https://anndata.dynverse.org/reference/AnnDataHelpers.md)
  [`py_to_r(`*`<anndata._core.sparse_dataset.SparseDataset>`*`)`](https://anndata.dynverse.org/reference/AnnDataHelpers.md)
  [`py_to_r(`*`<h5py._hl.dataset.Dataset>`*`)`](https://anndata.dynverse.org/reference/AnnDataHelpers.md)
  : AnnData Helpers
- [`dimnames(`*`<RawR6>`*`)`](https://anndata.dynverse.org/reference/RawHelpers.md)
  [`dim(`*`<RawR6>`*`)`](https://anndata.dynverse.org/reference/RawHelpers.md)
  [`as.matrix(`*`<RawR6>`*`)`](https://anndata.dynverse.org/reference/RawHelpers.md)
  [`r_to_py(`*`<RawR6>`*`)`](https://anndata.dynverse.org/reference/RawHelpers.md)
  [`py_to_r(`*`<anndata._core.raw.Raw>`*`)`](https://anndata.dynverse.org/reference/RawHelpers.md)
  [`` `[`( ``*`<RawR6>`*`)`](https://anndata.dynverse.org/reference/RawHelpers.md)
  : Raw Helpers
- [`all.equal(`*`<AnnDataR6>`*`)`](https://anndata.dynverse.org/reference/all.equal.md)
  [`all.equal(`*`<LayersR6>`*`)`](https://anndata.dynverse.org/reference/all.equal.md)
  [`all.equal(`*`<RawR6>`*`)`](https://anndata.dynverse.org/reference/all.equal.md)
  : Test if two objects objects are equal
- [`names(`*`<LayersR6>`*`)`](https://anndata.dynverse.org/reference/LayersHelpers.md)
  [`length(`*`<LayersR6>`*`)`](https://anndata.dynverse.org/reference/LayersHelpers.md)
  [`r_to_py(`*`<LayersR6>`*`)`](https://anndata.dynverse.org/reference/LayersHelpers.md)
  [`py_to_r(`*`<anndata._core.aligned_mapping.LayersBase>`*`)`](https://anndata.dynverse.org/reference/LayersHelpers.md)
  [`` `[`( ``*`<LayersR6>`*`)`](https://anndata.dynverse.org/reference/LayersHelpers.md)
  [`` `[<-`( ``*`<LayersR6>`*`)`](https://anndata.dynverse.org/reference/LayersHelpers.md)
  [`` `[[`( ``*`<LayersR6>`*`)`](https://anndata.dynverse.org/reference/LayersHelpers.md)
  [`` `[[<-`( ``*`<LayersR6>`*`)`](https://anndata.dynverse.org/reference/LayersHelpers.md)
  : Layers Helpers
- [`` `[[<-`( ``*`<collections.abc.MutableMapping>`*`)`](https://anndata.dynverse.org/reference/r-py-conversion.md)
  [`` `[[`( ``*`<collections.abc.Mapping>`*`)`](https://anndata.dynverse.org/reference/r-py-conversion.md)
  [`` `[<-`( ``*`<collections.abc.MutableMapping>`*`)`](https://anndata.dynverse.org/reference/r-py-conversion.md)
  [`` `[`( ``*`<collections.abc.Mapping>`*`)`](https://anndata.dynverse.org/reference/r-py-conversion.md)
  [`names(`*`<collections.abc.Mapping>`*`)`](https://anndata.dynverse.org/reference/r-py-conversion.md)
  [`py_to_r(`*`<collections.abc.Set>`*`)`](https://anndata.dynverse.org/reference/r-py-conversion.md)
  [`py_to_r(`*`<pandas.core.indexes.base.Index>`*`)`](https://anndata.dynverse.org/reference/r-py-conversion.md)
  [`py_to_r(`*`<collections.abc.KeysView>`*`)`](https://anndata.dynverse.org/reference/r-py-conversion.md)
  [`py_to_r(`*`<collections.abc.Mapping>`*`)`](https://anndata.dynverse.org/reference/r-py-conversion.md)
  [`py_to_r(`*`<anndata.abc._AbstractCSDataset>`*`)`](https://anndata.dynverse.org/reference/r-py-conversion.md)
  : Convert between Python and R objects

# Articles

### All vignettes

- [Getting
  started](https://anndata.dynverse.org/articles/getting_started.md):
- [Migrating from anndata to
  anndataR](https://anndata.dynverse.org/articles/migration_to_anndataR.md):
- [Demo with
  scanpy](https://anndata.dynverse.org/articles/scanpy_demo.md):