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AnnData-like live facade for a Daf object

Source: R/anndata_facade.R
DafAnnData.Rd

AnnData-like live facade for a Daf object

AnnData-like live facade for a Daf object

Details

Wraps a Daf object and provides AnnData-compatible accessors ($X, $obs, $var, $layers, $uns). This is a zero-copy live facade: reads are lazy and go through to the underlying Daf data on demand.

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 (obs_axis x var_axis)

  • $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)

All reads are lazy and cached via dafr's caching system.

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

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 (auto-detected if NULL)

var_axis

Variables axis name (auto-detected if NULL)

x_name

Primary matrix name (default "UMIs")

Method print()

Print the DafAnnData object

Usage

DafAnnData$print(...)

Arguments

...

Ignored

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.