anndata - Annotated Data

anndata provides a scalable way of keeping track of data and learned annotations, and can be used to read from and write to the h5ad file format. AnnData() stores a data matrix X together with annotations of observations obs (obsm, obsp), variables var (varm, varp), and unstructured annotations uns.

Details

This package is, in essense, an R wrapper for the similarly named Python package anndata, with some added functionality to support more R-like syntax. The version number of the anndata R package is synced with the version number of the python version.

Check out ?anndata for a full list of the functions provided by this package.

Creating an AnnData object

• AnnData()

Concatenating two or more AnnData objects

• concat()

Reading an AnnData object from a file

• read_csv()

• read_excel()

• read_h5ad()

• read_hdf()

• read_loom()

• read_mtx()

• read_text()

• read_umi_tools()

Writing an AnnData object to a file

• write_csvs()

• write_h5ad()

• write_loom()

Install the anndata Python package

• install_anndata()

See also

Useful links:

• https://anndata.dynverse.org

• https://github.com/dynverse/anndata

• Report bugs at https://github.com/dynverse/anndata/issues

Author

Maintainer: Robrecht Cannoodt rcannood@gmail.com (ORCID) (rcannood) [copyright holder]

Other contributors:

• Philipp Angerer phil.angerer@gmail.com (ORCID) (flying-sheep) [conceptor]

• Alex Wolf f.alex.wolf@gmx.de (ORCID) (falexwolf) [conceptor]

• Isaac Virshup (ivirshup) [conceptor]

• Sergei Rybakov (Koncopd) [conceptor]

Examples

if (FALSE) { # \dontrun{
ad <- AnnData(
  X = matrix(1:6, nrow = 2),
  obs = data.frame(group = c("a", "b"), row.names = c("s1", "s2")),
  var = data.frame(type = c(1L, 2L, 3L), row.names = c("var1", "var2", "var3")),
  layers = list(
    spliced = matrix(4:9, nrow = 2),
    unspliced = matrix(8:13, nrow = 2)
  ),
  obsm = list(
    ones = matrix(rep(1L, 10), nrow = 2),
    rand = matrix(rnorm(6), nrow = 2),
    zeros = matrix(rep(0L, 10), nrow = 2)
  ),
  varm = list(
    ones = matrix(rep(1L, 12), nrow = 3),
    rand = matrix(rnorm(6), nrow = 3),
    zeros = matrix(rep(0L, 12), nrow = 3)
  ),
  uns = list(
    a = 1,
    b = data.frame(i = 1:3, j = 4:6, value = runif(3)),
    c = list(c.a = 3, c.b = 4)
  )
)

ad$X

ad$obs
ad$var

ad$obsm["ones"]
ad$varm["rand"]

ad$layers["unspliced"]
ad$layers["spliced"]

ad$uns["b"]

ad[, c("var1", "var2")]
ad[-1, , drop = FALSE]
ad[, 2] <- 10
} # }