AnnData-like live facade for a Daf object

AnnData-like live facade for a Daf object

AnnData-like live facade for a Daf object

Value

An R6 object of class DafAnnData.

Details

Wraps a Daf object and provides AnnData-compatible accessors ($X, $obs, $var, $layers, $uns). This is a read-only facade: reads are lazy and go through to the underlying Daf object on demand, benefiting from dafJuliaWrapper's R-side caching.

The facade maps AnnData concepts to Daf data:

• $X - the primary matrix (obs_axis x var_axis, named x_name)

• $obs - data frame of observation (obs_axis) vectors

• $var - data frame of variable (var_axis) vectors

• $layers - named list of additional matrices (excluding $X)

• $uns - named list of scalars

• $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 - c(n_obs, n_vars)

Public fields

daf

The underlying Daf object

obs_axis

Name of the observations axis

var_axis

Name of the variables axis

x_name

Name of the primary matrix

Active bindings

X

The primary matrix (obs x var)

obs

Data frame of observation vectors

var

Data frame of variable vectors

layers

Named list of additional matrices (excluding X)

uns

Named list of scalars

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)

Methods

Public methods

• DafAnnData$new()

• DafAnnData$print()

• DafAnnData$summary()

• DafAnnData$clone()

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Method new()

Create a new DafAnnData facade.

Usage

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

Arguments

daf

A Daf object

obs_axis

Observations axis name. If NULL, auto-detects "cell" or "metacell".

var_axis

Variables axis name. If NULL, auto-detects "gene".

x_name

Primary matrix name. If NULL, the first matrix available on (obs_axis, var_axis) is used; defaults to "UMIs" when present.

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Method print()

Print a concise summary. Prints dimensions and axis names only; call summary() for the full listing of obs/var/layer names.

Usage

DafAnnData$print(...)

Arguments

...

Ignored.

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Method summary()

Full listing of obs vectors, var vectors, and layer names. Each access is a bridge call; kept out of print() to keep auto-print cheap.

Usage

DafAnnData$summary(object, ...)

Arguments

object

Present for S3 generic compatibility.

...

Ignored.

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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.