Package 'cellxgene.census'

Download source H5AD to local file name.

Description

Download source H5AD to local file name.

Usage

download_source_h5ad(
  dataset_id,
  file,
  overwrite = FALSE,
  census_version = "stable",
  census = NULL
)

Arguments

dataset_id	The dataset_id of interest.
file	Local file name to store H5AD file.
overwrite	TRUE to allow overwriting an existing file.
census_version	The desired Census version.
census	An open Census handle for census_version. If not provided, then it will be opened and closed automatically; but it's more efficient to reuse a handle if calling download_source_h5ad() multiple times.

Examples

download_source_h5ad("0895c838-e550-48a3-a777-dbcd35d30272", "/tmp/data.h5ad", overwrite = TRUE)

---

Get locator information about a Census mirror

Description

Get locator information about a Census mirror

Usage

get_census_mirror(mirror)

Arguments

mirror

Name of the mirror.

Value

List with mirror information

Examples

get_census_mirror("AWS-S3-us-west-2")

---

Get the directory of Census mirrors currently available

Description

Get the directory of Census mirrors currently available

Usage

get_census_mirror_directory()

Value

Nested list with information about available mirrors

Examples

get_census_mirror_directory()

---

Get release description for a Census version

Description

Get release description for a Census version

Usage

get_census_version_description(census_version)

Arguments

census_version

The census version name.

Value

List with the release location and metadata

Examples

as.data.frame(get_census_version_description("stable"))

---

Get the directory of Census releases currently available

Description

Get the directory of Census releases currently available

Usage

get_census_version_directory()

Value

Data frame of available cell census releases, including location and metadata.

Examples

get_census_version_directory()

---

Read the feature dataset presence matrix.

Description

Read the feature dataset presence matrix.

Usage

get_presence_matrix(census, organism, measurement_name = "RNA")

Arguments

census	The census object from cellxgene.census::open_soma().
organism	The organism to query, usually one of ⁠Homo sapiens⁠ or ⁠Mus musculus⁠
measurement_name	The measurement object to query. Defaults to RNA.

Value

A tiledbsoma::matrixZeroBasedView object with dataset join id & feature join id dimensions, filled with 1s indicating presence. The sparse matrix is accessed with zero-based indexes since the join id's may be zero.

Examples

census <- open_soma()
on.exit(census$close(), add = TRUE)
print(get_presence_matrix(census, "Homo sapiens")$dim())

---

Export Census slices to Seurat

Description

Convenience wrapper around SOMAExperimentAxisQuery, to build and execute a query, and return it as a Seurat object.

Usage

get_seurat(
  census,
  organism,
  measurement_name = "RNA",
  X_layers = c(counts = "raw", data = NULL),
  obs_value_filter = NULL,
  obs_coords = NULL,
  obs_column_names = NULL,
  obsm_layers = FALSE,
  var_value_filter = NULL,
  var_coords = NULL,
  var_column_names = NULL,
  var_index = "feature_id"
)

Arguments

census	The census object, usually returned by cellxgene.census::open_soma().
organism	The organism to query, usually one of ⁠Homo sapiens⁠ or ⁠Mus musculus⁠
measurement_name	The measurement object to query. Defaults to RNA.
X_layers	A named character of X layers to add to the Seurat assay, where the names are the names of Seurat slots (counts or data) and the values are the names of layers within X.
obs_value_filter	A SOMA value_filter across columns in the obs dataframe, expressed as string.
obs_coords	A set of coordinates on the obs dataframe index, expressed in any type or format supported by SOMADataFrame's read() method.
obs_column_names	Columns to fetch for the obs data frame.
obsm_layers	Names of arrays in obsm to add as the cell embeddings; pass FALSE to suppress loading in any dimensional reductions.
var_value_filter	Same as obs_value_filter but for var.
var_coords	Same as obs_coords but for var.
var_column_names	Columns to fetch for the var data frame.
var_index	Name of column in ‘var’ to add as feature names.

Value

A Seurat object containing the sensus slice.

Examples

## Not run: 
census <- open_soma()
seurat_obj <- get_seurat(
  census,
  organism = "Homo sapiens",
  obs_value_filter = "cell_type == 'leptomeningeal cell'",
  var_value_filter = "feature_id %in% c('ENSG00000107317', 'ENSG00000106034')"
)

seurat_obj

census$close()

## End(Not run)

---

Export Census slices to SingleCellExperiment

Description

Convenience wrapper around SOMAExperimentAxisQuery, to build and execute a query, and return it as a SingleCellExperiment object.

Usage

get_single_cell_experiment(
  census,
  organism,
  measurement_name = "RNA",
  X_layers = c(counts = "raw"),
  obs_value_filter = NULL,
  obs_coords = NULL,
  obs_column_names = NULL,
  obsm_layers = FALSE,
  var_value_filter = NULL,
  var_coords = NULL,
  var_column_names = NULL,
  var_index = "feature_id"
)

Arguments

census	The census object, usually returned by cellxgene.census::open_soma().
organism	The organism to query, usually one of ⁠Homo sapiens⁠ or ⁠Mus musculus⁠
measurement_name	The measurement object to query. Defaults to RNA.
X_layers	A character vector of X layers to add as assays in the main experiment; may optionally be named to set the name of the resulting assay (eg. ‘X_layers = c(counts = "raw")’ will load in X layer “‘raw’” as assay “‘counts’”); by default, loads in all X layers
obs_value_filter	A SOMA value_filter across columns in the obs dataframe, expressed as string.
obs_coords	A set of coordinates on the obs dataframe index, expressed in any type or format supported by SOMADataFrame's read() method.
obs_column_names	Columns to fetch for the obs data frame.
obsm_layers	Names of arrays in obsm to add as the cell embeddings; pass FALSE to suppress loading in any dimensional reductions.
var_value_filter	Same as obs_value_filter but for var.
var_coords	Same as obs_coords but for var.
var_column_names	Columns to fetch for the var data frame.
var_index	Name of column in ‘var’ to add as feature names.

Value

A SingleCellExperiment object containing the sensus slice.

Examples

## Not run: 
census <- open_soma()
sce_obj <- get_single_cell_experiment(
  census,
  organism = "Homo sapiens",
  obs_value_filter = "cell_type == 'leptomeningeal cell'",
  var_value_filter = "feature_id %in% c('ENSG00000107317', 'ENSG00000106034')"
)

sce_obj

census$close()

## End(Not run)

---

Locate source h5ad file for a dataset.

Description

Locate source h5ad file for a dataset.

Usage

get_source_h5ad_uri(dataset_id, census_version = "stable", census = NULL)

Arguments

dataset_id	The dataset_id of interest.
census_version	The desired Census version.
census	An open Census handle for census_version. If not provided, then it will be opened and closed automatically; but it's more efficient to reuse a handle if calling get_source_h5ad_uri() multiple times.

Value

A list with uri and optional s3_region.

Examples

get_source_h5ad_uri("0895c838-e550-48a3-a777-dbcd35d30272")

---

Create SOMATileDBContext for Census

Description

Create a SOMATileDBContext suitable for using with open_soma(). Typically open_soma() creates a context automatically, but one can be created separately in order to set custom configuration options, or to share it between multiple open Census handles.

Usage

new_SOMATileDBContext_for_census(
  census_version_description,
  mirror = "default",
  ...
)

Arguments

census_version_description	The result of get_census_version_description() for the desired Census version.
mirror	The name of the intended census mirror (or get_census_mirror_directory()[[name]] to save the lookup), or NULL to configure for local file access.
...	Custom configuration options.

Value

SOMATileDBContext object for open_soma().

Examples

census_desc <- get_census_version_description("stable")
ctx <- new_SOMATileDBContext_for_census(census_desc, "soma.init_buffer_bytes" = paste(4 * 1024**3))
census <- open_soma("stable", tiledbsoma_ctx = ctx)
census$close()

---

Open the Census

Description

Open the Census

Usage

open_soma(
  census_version = "stable",
  uri = NULL,
  tiledbsoma_ctx = NULL,
  mirror = NULL
)

Arguments

census_version	The version of the Census, e.g., "stable".
uri	A URI containing the Census SOMA objects to open instead of a released version. (If supplied, takes precedence over census_version.)
tiledbsoma_ctx	A tiledbsoma::SOMATileDBContext built using new_SOMATileDBContext_for_census(). Optional (created automatically) if using census_version and the context does not need to be reused.
mirror	The Census mirror to access; one of names(get_census_mirror_directory()).

Value

Top-level tiledbsoma::SOMACollection object. After use, the census should be closed to release memory and other resources, usually with on.exit(census$close(), add = TRUE). Closing the top-level census will also close all SOMA objects accessed through it.

Examples

census <- open_soma()
as.data.frame(census$get("census_info")$get("summary")$read()$concat())
census$close()

---