Read-only AnnData-shaped facade over a Daf.

Read-only AnnData-shaped facade over a Daf.

Read-only AnnData-shaped facade over a Daf.

Details

Exposes a DafReader through the property names familiar to anndata / scanpy / Seurat users: X, obs, var, layers, uns, obs_names, var_names, n_obs, n_vars, shape. All bindings are read-only; modifying data requires writing to the underlying Daf directly.

See also

as_anndata()

Public fields

daf

The underlying Daf object.

obs_axis

Name of the observations axis.

var_axis

Name of the variables axis.

x_name

Matrix name for X.

Active bindings

X

The primary matrix (obs_axis x var_axis).

obs

Data frame of observation vectors.

var

Data frame of variable vectors.

obs_names

Character vector of observation names.

var_names

Character vector of variable names.

n_obs

Number of observations.

n_vars

Number of variables.

shape

Dimensions c(n_obs, n_vars).

layers

Named list of additional matrices (excluding X).

uns

Named list of scalars.

Methods

Public methods

• DafAnnData$new()

• DafAnnData$clone()

---

Method new()

Create a DafAnnData facade.

Usage

DafAnnData$new(daf, obs_axis = NULL, var_axis = NULL, x_name = "UMIs")

Arguments

daf

A DafReader.

obs_axis

Axis name for observations. Defaults auto-detect: "cell" then "metacell".

var_axis

Axis name for variables. Defaults to "gene".

x_name

Matrix name for X. Default "UMIs".

---

Method clone()

The objects of this class are cloneable with this method.

Usage

DafAnnData$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

d <- memory_daf()
add_axis(d, "cell", c("c1", "c2"))
add_axis(d, "gene", c("g1", "g2", "g3"))
set_matrix(d, "cell", "gene", "UMIs", matrix(1:6, 2, 3))
ann <- as_anndata(d)
ann$X
#>    g1 g2 g3
#> c1  1  3  5
#> c2  2  4  6
ann$obs_names
#> [1] "c1" "c2"