AnnData Helpers

AnnData Helpers

Usage

# S3 method for AnnDataR6
dimnames(x)

# S3 method for AnnDataR6
dimnames(x) <- value

# S3 method for AnnDataR6
dim(x)

# S3 method for AnnDataR6
as.data.frame(x, row.names = NULL, optional = FALSE, layer = NULL, ...)

# S3 method for AnnDataR6
as.matrix(x, layer = NULL, ...)

# S3 method for AnnDataR6
r_to_py(x, convert = FALSE)

# S3 method for anndata._core.anndata.AnnData
py_to_r(x)

# S3 method for AnnDataR6
[(x, oidx, vidx)

# S3 method for AnnDataR6
t(x)

# S3 method for anndata._core.sparse_dataset.SparseDataset
py_to_r(x)

# S3 method for h5py._hl.dataset.Dataset
py_to_r(x)

Arguments

x

An AnnData object.

value

a possible valie for dimnames(ad). The dimnames of a AnnData can be NULL (which is not stored) or a list of the same length as dim(ad). If a list, its components are either NULL or a character vector with positive length of the appropriate dimension of ad.

row.names

Not used.

optional

Not used.

layer

An AnnData layer. If NULL, will use ad$X, otherwise ad$layers[layer].

...

Parameters passed to the underlying function.

convert

Not used.

oidx

Observation indices

vidx

Variable indices

Examples

if (FALSE) {
ad <- AnnData(
  X = matrix(c(0, 1, 2, 3, 4, 5), 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(c(4, 5, 6, 7, 8, 9), nrow = 2),
    unspliced = matrix(c(8, 9, 10, 11, 12, 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 = 2, c = list(c.a = 3, c.b = 4))
)

dimnames(ad)
dim(ad)
as.data.frame(ad)
as.data.frame(ad, layer = "unspliced")
as.matrix(ad)
as.matrix(ad, layer = "unspliced")
ad[2,,drop=FALSE]
ad[,-1]
ad[,c("var1", "var2")]
}