Raw {anndata}R Documentation

Create a Raw object

Description

Create a Raw object

Usage

Raw(adata, X = NULL, var = NULL, varm = NULL)

Arguments

adata

An AnnData object.

X

A #observations × #variables data matrix.

var

Key-indexed one-dimensional variables annotation of length #variables.

varm

Key-indexed multi-dimensional variables annotation of length #variables.

Active bindings

X

Data matrix of shape n_obs × n_vars.

n_obs

Number of observations.

obs_names

Names of observations.

n_vars

Number of variables.

var

One-dimensional annotation of variables (data.frame).

var_names

Names of variables.

varm

Multi-dimensional annotation of variables (matrix).

Stores for each key a two or higher-dimensional matrix with n_var rows.

shape

Shape of data matrix (n_obs, n_vars).

Methods

Public methods

Method new()

Create a new Raw object

Usage
RawR6$new(obj)
Arguments
obj

A Python Raw object

Method copy()

Full copy, optionally on disk.

Usage
RawR6$copy()
Arguments
filename

Path to filename (default: NULL).

Examples
\dontrun{
ad <- AnnData(
  X = matrix(c(0, 1, 2, 3), nrow = 2)
)
ad$copy()
ad$copy("file.h5ad")
}

Method to_adata()

Create a full AnnData object

Usage
RawR6$to_adata()
Examples
\dontrun{
ad <- AnnData(
  X = matrix(c(0, 1, 2, 3), nrow = 2),
  obs = data.frame(group = c("a", "b"), row.names = c("s1", "s2")),
  var = data.frame(type = c(1L, 2L), row.names = c("var1", "var2")),
  layers = list(
    spliced = matrix(c(4, 5, 6, 7), nrow = 2),
    unspliced = matrix(c(8, 9, 10, 11), nrow = 2)
  )
)
ad$raw <- ad

ad$raw$to_adata()
}

Method print()

Print Raw object

Usage
RawR6$print(...)
Arguments
...

optional arguments to print method.

Examples
\dontrun{
ad <- AnnData(
  X = matrix(c(0, 1, 2, 3), nrow = 2),
  obs = data.frame(group = c("a", "b"), row.names = c("s1", "s2")),
  var = data.frame(type = c(1L, 2L), row.names = c("var1", "var2")),
  layers = list(
    spliced = matrix(c(4, 5, 6, 7), nrow = 2),
    unspliced = matrix(c(8, 9, 10, 11), 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, 10), nrow = 2),
    rand = matrix(rnorm(6), nrow = 2),
    zeros = matrix(rep(0L, 10), nrow = 2)
  ),
  uns = list(a = 1, b = 2, c = list(c.a = 3, c.b = 4))
)
ad$raw <- ad

library(reticulate)
sc <- import("scanpy")
sc$pp$normalize_per_cell(ad)

ad[]
ad$raw[]

ad$print()
print(ad)
}

Method .set_py_object()

Set internal Python object

Usage
RawR6$.set_py_object(obj)
Arguments
obj

A Python Raw object

Method .get_py_object()

Get internal Python object

Usage
RawR6$.get_py_object()

Examples

## Not run: 
ad <- AnnData(
  X = matrix(c(0, 1, 2, 3), nrow = 2),
  obs = data.frame(group = c("a", "b"), row.names = c("s1", "s2")),
  var = data.frame(type = c(1L, 2L), row.names = c("var1", "var2")),
  layers = list(
    spliced = matrix(c(4, 5, 6, 7), nrow = 2),
    unspliced = matrix(c(8, 9, 10, 11), 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, 10), nrow = 2),
    rand = matrix(rnorm(6), nrow = 2),
    zeros = matrix(rep(0L, 10), nrow = 2)
  ),
  uns = list(a = 1, b = 2, c = list(c.a = 3, c.b = 4))
)
ad$raw <- ad

library(reticulate)
sc <- import("scanpy")
sc$pp$normalize_per_cell(ad)

ad[]
ad$raw[]

## End(Not run)

## ------------------------------------------------
## Method `RawR6$copy`
## ------------------------------------------------

## Not run: 
ad <- AnnData(
  X = matrix(c(0, 1, 2, 3), nrow = 2)
)
ad$copy()
ad$copy("file.h5ad")

## End(Not run)

## ------------------------------------------------
## Method `RawR6$to_adata`
## ------------------------------------------------

## Not run: 
ad <- AnnData(
  X = matrix(c(0, 1, 2, 3), nrow = 2),
  obs = data.frame(group = c("a", "b"), row.names = c("s1", "s2")),
  var = data.frame(type = c(1L, 2L), row.names = c("var1", "var2")),
  layers = list(
    spliced = matrix(c(4, 5, 6, 7), nrow = 2),
    unspliced = matrix(c(8, 9, 10, 11), nrow = 2)
  )
)
ad$raw <- ad

ad$raw$to_adata()

## End(Not run)

## ------------------------------------------------
## Method `RawR6$print`
## ------------------------------------------------

## Not run: 
ad <- AnnData(
  X = matrix(c(0, 1, 2, 3), nrow = 2),
  obs = data.frame(group = c("a", "b"), row.names = c("s1", "s2")),
  var = data.frame(type = c(1L, 2L), row.names = c("var1", "var2")),
  layers = list(
    spliced = matrix(c(4, 5, 6, 7), nrow = 2),
    unspliced = matrix(c(8, 9, 10, 11), 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, 10), nrow = 2),
    rand = matrix(rnorm(6), nrow = 2),
    zeros = matrix(rep(0L, 10), nrow = 2)
  ),
  uns = list(a = 1, b = 2, c = list(c.a = 3, c.b = 4))
)
ad$raw <- ad

library(reticulate)
sc <- import("scanpy")
sc$pp$normalize_per_cell(ad)

ad[]
ad$raw[]

ad$print()
print(ad)

## End(Not run)
[Package anndata version 0.7.5.6 Index]