Package 'tiledbsoma'

Title: TileDB SOMA
Description: Interface for working with 'TileDB'-based Stack of Matrices, Annotated ('SOMA'): an open data model for representing annotated matrices, like those commonly used for single cell data analysis.
Authors: Aaron Wolen [cre, aut] , Dirk Eddelbuettel [aut] , Paul Hoffman [aut] , John Kerl [aut], TileDB, Inc. [cph, fnd]
Maintainer: Aaron Wolen <[email protected]>
License: MIT + file LICENSE
Version: 0.99.4
Built: 2024-10-27 02:57:04 UTC
Source: https://github.com/single-cell-data/TileDB-SOMA

Help Index

A Configuration List

Description

An R6 mapping type for configuring various “parameters”. Essentially, serves as a nested map where the inner map is a ScalarMap: {<param>: {<key>: <value>}}

Super class

tiledbsoma::MappingBase -> ConfigList

Methods

Public methods

Inherited methods

Method get()

Usage
ConfigList$get(param, key = NULL, default = quote(expr = ))
Arguments
param

Outer key or “parameter” to fetch

key

Inner key to fetch; pass NULL to return the map for param

default

Default value to fetch if key is not found; defaults to NULL

Returns

The value of key for param in the map, or default if key is not found

Method set()

Usage
ConfigList$set(param, key, value)
Arguments
param

Outer key or “parameter” to set

key

Inner key to set

value

Value to add for key, or NULL to remove the entry for key; optionally provide only param and value as a ScalarMap to update param with the keys and values from value

Returns

\[chainable\] Invisibly returns self with value added for key in param

Method setv()

Usage
ConfigList$setv(...)
Arguments
...

Ignored

Returns

Nothing; setv() is disabled for ConfigList objects

Method clone()

The objects of this class are cloneable with this method.

Usage
ConfigList$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

SOMA Example Datasets

Description

Access example SOMA objects bundled with the tiledbsoma package.

Use list_datasets() to list the available datasets and load_dataset() to load a dataset into memory using the appropriate SOMA class. The extract_dataset() method returns the path to the extracted dataset without loading it into memory.

Usage

list_datasets()

extract_dataset(name, dir = tempdir())

load_dataset(name, dir = tempdir(), tiledbsoma_ctx = NULL)

Arguments

name

The name of the dataset.
dir

The directory where the dataset will be extracted to (default: tempdir()).
tiledbsoma_ctx

Optional TileDB ‘Context’ object, defaults to NULL

Details

The SOMA objects are stored as tar.gz files in the package's extdata directory. Calling load_dataset() extracts the tar.gz file to the specified dir, inspects its metadata to determine the appropriate SOMA class to instantiate, and returns the SOMA object.

Value

  • list_datasets() returns a character vector of the available datasets.

  • extract_dataset() returns the path to the extracted dataset.

  • load_dataset() returns a SOMA object.

Examples

soma_pbmc_small <- load_dataset("soma-exp-pbmc-small")

matrixZeroBasedView is a wrapper shim for a matrix or Matrix::sparseMatrix providing

Description

matrixZeroBasedView is a class that allows elemental matrix access using zero-based indeces.

Methods

Public methods

Method new()

Initialize (lifecycle: experimental)

Usage
matrixZeroBasedView$new(x)
Arguments
x

matrix or Matrix::sparseMatrix or Matrix::Matrix

Method take()

Zero-based matrix element access

Usage
matrixZeroBasedView$take(i = NULL, j = NULL)
Arguments
i

Row index (zero-based).

j

Column index (zero-based).

Returns

The specified matrix slice as another matrixZeroBasedView

Method dim()

dim

Usage
matrixZeroBasedView$dim()
Returns

The dimensions of the matrix.

Method nrow()

nrow

Usage
matrixZeroBasedView$nrow()
Returns

Matrix row count.

Method ncol()

ncol

Usage
matrixZeroBasedView$ncol()
Returns

Matrix column count.

Method get_one_based_matrix()

Get the one-based R matrix with its original class

Usage
matrixZeroBasedView$get_one_based_matrix()
Returns

One-based matrix

Method sum()

Perform arithmetic sum between this linkmatrixZeroBasedView and another linkmatrixZeroBasedView.

Usage
matrixZeroBasedView$sum(x)
Arguments
x

the linkmatrixZeroBasedView to sum.

Returns

The result of the sum as a matrixZeroBasedView.

Method print()

print

Usage
matrixZeroBasedView$print()

Method clone()

The objects of this class are cloneable with this method.

Usage
matrixZeroBasedView$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Platform Configuration

Description

An R6 mapping type for configuring various “parameters” for multiple “platforms”, essentially serves a multi-nested map where the inner map is a ScalarMap contained within a ConfigList (middle map): {platform: {param: {key: value}}}

Super class

tiledbsoma::MappingBase -> PlatformConfig

Methods

Public methods

Inherited methods

Method platforms()

Usage
PlatformConfig$platforms()
Returns

The names of the “platforms” (outer keys)

Method params()

Usage
PlatformConfig$params(platform = NULL)
Arguments
platform

The “platform” to pull parameter names (middle keys) for; pass TRUE to return all possible parameter names

Returns

The parameter names (middle keys) for platform

Method get()

Usage
PlatformConfig$get(
  platform,
  param = NULL,
  key = NULL,
  default = quote(expr = )
)
Arguments
platform

The name of the “platform” (outer key) to fetch

param

The name of the “paramters” of platform to fetch; if NULL, returns the configuration for platform

key

The “key” (inner key) for param in platform to fetch; if NULL and param is passed, returns the map for param in platform

default

Default value to fetch if key is not found; defaults to null

Returns

The value of key for param in platform in the map, or default if key is not found

Method get_params()

Usage
PlatformConfig$get_params(platform)
Arguments
platform

The name of the “platform” (outer key) to fetch

Returns

The ConfigList for platform

Method set()

Usage
PlatformConfig$set(platform, param, key, value)
Arguments
platform

The name of the “platform” (outer key) to set

param

Name of the “parameter” (middle key) in platform to set

key

Inner key to set

value

Value to add for key, or NULL to remove the entry for key; optionally provide only platfomr, param, and value as a ScalarMap to update param for platform with the keys and values from value

Returns

\[chainable\] Invisibly returns self with value added for key in param for platform

Method setv()

Usage
PlatformConfig$setv(...)
Arguments
...

Ignored

Returns

Nothing; setv() is disabled for PlatformConfig objects

Method clone()

The objects of this class are cloneable with this method.

Usage
PlatformConfig$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Display package versions

Description

Print version information for tiledb (R package), libtiledbsoma, and TileDB embedded, suitable for assisting with bug reports.

Usage

show_package_versions()

SOMA Axis Query

Description

Construct a single-axis query object with a combination of coordinates and/or value filters for use with SOMAExperimentAxisQuery. (lifecycle: experimental)

Per dimension, the SOMAAxisQuery can have value of:

  • None (i.e., coords = NULL and value_filter = NULL) - read all values

  • Coordinates - a set of coordinates on the axis dataframe index, expressed in any type or format supported by SOMADataFrame's read() method.

  • A SOMA value_filter across columns in the axis dataframe, expressed as string

  • Or, a combination of coordinates and value filter.

Public fields

coords

The coordinates for the query.

value_filter

The value filter for the query.

Methods

Public methods

Method new()

Create a new SOMAAxisQuery object.

Usage
SOMAAxisQuery$new(value_filter = NULL, coords = NULL)
Arguments
value_filter

Optional string containing a logical expression that is used to filter the returned values.

coords

Optional indices specifying the rows to read: either a vector of the appropriate type or a named list of vectors corresponding to each dimension.

Method clone()

The objects of this class are cloneable with this method.

Usage
SOMAAxisQuery$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

tiledb::parse_query_condition() for more information about valid value filters.

SOMAExperiment Axis Query Result

Description

Access SOMAExperimentAxisQuery results.

Active bindings

obs

arrow::Table containing obs query slice.

var

arrow::Table containing var query slice. measurement_name.

X_layers

named list of arrow::Tables for each X layer.

Methods

Public methods

Method new()

Create a new SOMAAxisQueryResult object.

Usage
SOMAAxisQueryResult$new(obs, var, X_layers)
Arguments
obs, var

arrow::Table containing obs or var query slice.

X_layers

named list of arrow::Tables, one for each X layer.

Method clone()

The objects of this class are cloneable with this method.

Usage
SOMAAxisQueryResult$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

SOMA Collection

Description

Contains a key-value mapping where the keys are string names and the values are any SOMA-defined foundational or composed type, including SOMACollection, SOMADataFrame, SOMADenseNDArray, SOMASparseNDArray, or SOMAExperiment. (lifecycle: experimental)

Super classes

tiledbsoma::TileDBObject -> tiledbsoma::TileDBGroup -> tiledbsoma::SOMACollectionBase -> SOMACollection

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
SOMACollection$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Create SOMA Collection

Description

Factory function to create a SOMADataFrame for writing, (lifecycle: experimental)

Usage

SOMACollectionCreate(
  uri,
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp

Open SOMA Collection

Description

Factory function to open a SOMACollection for reading, (lifecycle: experimental)

Usage

SOMACollectionOpen(
  uri,
  mode = "READ",
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
mode

One of "READ" or "WRITE"
platform_config

Optional platform configuration
tiledbsoma_ctx

optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp. In READ mode, defaults to the current time. If non-NULL, then all members accessed through the collection object inherit the timestamp.

SOMADataFrame

Description

SOMADataFrame is a multi-column table that must contain a column called soma_joinid of type int64, which contains a unique value for each row and is intended to act as a join key for other objects, such as SOMASparseNDArray. (lifecycle: experimental)

Super classes

tiledbsoma::TileDBObject -> tiledbsoma::TileDBArray -> tiledbsoma::SOMAArrayBase -> SOMADataFrame

Methods

Public methods

Inherited methods

Method create()

Create (lifecycle: experimental)

Usage
SOMADataFrame$create(
  schema,
  index_column_names = c("soma_joinid"),
  platform_config = NULL,
  internal_use_only = NULL
)
Arguments
schema

an arrow::schema.

index_column_names

A vector of column names to use as user-defined index columns. All named columns must exist in the schema, and at least one index column name is required.

platform_config

A platform configuration object

internal_use_only

Character value to signal this is a 'permitted' call, as create() is considered internal and should not be called directly.

Method write()

Write (lifecycle: experimental)

Usage
SOMADataFrame$write(values)
Arguments
values

An arrow::Table or arrow::RecordBatch containing all columns, including any index columns. The schema for values must match the schema for the SOMADataFrame.

Method read()

Read (lifecycle: experimental) Read a user-defined subset of data, addressed by the dataframe indexing column, and optionally filtered.

Usage
SOMADataFrame$read(
  coords = NULL,
  column_names = NULL,
  value_filter = NULL,
  result_order = "auto",
  iterated = FALSE,
  log_level = "auto"
)
Arguments
coords

Optional named list of indices specifying the rows to read; each (named) list element corresponds to a dimension of the same name.

column_names

Optional character vector of column names to return.

value_filter

Optional string containing a logical expression that is used to filter the returned values. See tiledb::parse_query_condition for more information.

result_order

Optional order of read results. This can be one of either ⁠"ROW_MAJOR, ⁠"COL_MAJOR"⁠, or ⁠"auto"' (default).

iterated

Option boolean indicated whether data is read in call (when FALSE, the default value) or in several iterated steps.

log_level

Optional logging level with default value of "warn".

Returns

arrow::Table or TableReadIter

Method clone()

The objects of this class are cloneable with this method.

Usage
SOMADataFrame$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Create SOMA DataFrame

Description

Factory function to create a SOMADataFrame for writing, (lifecycle: experimental)

Usage

SOMADataFrameCreate(
  uri,
  schema,
  index_column_names = c("soma_joinid"),
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
schema

schema Arrow schema argument passed on to DataFrame$create()
index_column_names

Index column names passed on to DataFrame$create()
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp

Open SOMA DataFrame

Description

Factory function to open a SOMADataFrame for reading, (lifecycle: experimental)

Usage

SOMADataFrameOpen(
  uri,
  mode = "READ",
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
mode

One of "READ" or "WRITE"
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp

SOMADenseNDArray

Description

SOMADenseNDArray is a dense, N-dimensional array of primitive type, with offset (zero-based) int64 integer indexing on each dimension with domain ⁠[0, maxInt64)⁠. The SOMADenseNDArray has a user-defined schema, which includes:

  • type: a primitive type, expressed as an Arrow type (e.g., int64, float32, etc), indicating the type of data contained within the array

  • shape: the shape of the array, i.e., number and length of each dimension

All dimensions must have a positive, non-zero length, and there must be 1 or more dimensions.

The default "fill" value for SOMADenseNDArray is the zero or null value of the array type (e.g., Arrow.float32 defaults to 0.0).

The write method is currently limited to writing from 2-d matrices. (lifecycle: experimental)

Super classes

tiledbsoma::TileDBObject -> tiledbsoma::TileDBArray -> tiledbsoma::SOMAArrayBase -> tiledbsoma::SOMANDArrayBase -> SOMADenseNDArray

Methods

Public methods

Inherited methods

Method read_arrow_table()

Read as an 'arrow::Table' (lifecycle: experimental)

Usage
SOMADenseNDArray$read_arrow_table(
  coords = NULL,
  result_order = "auto",
  log_level = "warn"
)
Arguments
coords

Optional list of integer vectors, one for each dimension, with a length equal to the number of values to read. If NULL, all values are read. List elements can be named when specifying a subset of dimensions.

result_order

Optional order of read results. This can be one of either ⁠"ROW_MAJOR, ⁠"COL_MAJOR"⁠, or ⁠"auto"' (default).

result_order

Optional order of read results. This can be one of either ⁠"ROW_MAJOR, ⁠"COL_MAJOR"⁠, or ⁠"auto"' (default).

log_level

Optional logging level with default value of "warn".

Returns

An arrow::Table.

Method read_dense_matrix()

Read as a dense matrix (lifecycle: experimental)

Usage
SOMADenseNDArray$read_dense_matrix(
  coords = NULL,
  result_order = "ROW_MAJOR",
  log_level = "warn"
)
Arguments
coords

Optional list of integer vectors, one for each dimension, with a length equal to the number of values to read. If NULL, all values are read. List elements can be named when specifying a subset of dimensions.

result_order

Optional order of read results. This can be one of either ⁠"ROW_MAJOR, ⁠"COL_MAJOR"⁠, or ⁠"auto"' (default).

result_order

Optional order of read results. This can be one of either ⁠"ROW_MAJOR, ⁠"COL_MAJOR"⁠, or ⁠"auto"' (default).

log_level

Optional logging level with default value of "warn".

Returns

A matrix object

Method write()

Write matrix data to the array. (lifecycle: experimental)

More general write methods for higher-dimensional array could be added.

Usage
SOMADenseNDArray$write(values, coords = NULL)
Arguments
values

A matrix. Character dimension names are ignored because SOMANDArray's use integer indexing.

coords

A list of integer vectors, one for each dimension, with a length equal to the number of values to write. If NULL, the default, the values are taken from the row and column names of values.

Method clone()

The objects of this class are cloneable with this method.

Usage
SOMADenseNDArray$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Create SOMA Dense Nd Array

Description

Factory function to create a SOMADenseNDArray for writing, (lifecycle: experimental)

Usage

SOMADenseNDArrayCreate(
  uri,
  type,
  shape,
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
type

An Arrow type defining the type of each element in the array.
shape

A vector of integers defining the shape of the array.
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp

Open SOMA Dense Nd Array

Description

Factory function to open a SOMADenseNDArray for reading, (lifecycle: experimental)

Usage

SOMADenseNDArrayOpen(
  uri,
  mode = "READ",
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
mode

One of "READ" or "WRITE"
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp

SOMA Experiment

Description

SOMAExperiment is a specialized SOMACollection, representing one or more modes of measurement across a single collection of cells (aka a "multimodal dataset") with pre-defined fields: obs and ms (see Active Bindings below for details). (lifecycle: experimental)

Adding new objects to a collection

The SOMAExperiment class provides a number of type-specific methods for adding new a object to the collection, such as add_new_sparse_ndarray() and add_new_dataframe(). These methods will create the new object and add it as member of the SOMAExperiment. The new object will always inherit the parent context (see SOMATileDBContext) and, by default, its platform configuration (see PlatformConfig). However, the user can override the default platform configuration by passing a custom configuration to the platform_config argument.

Super classes

tiledbsoma::TileDBObject -> tiledbsoma::TileDBGroup -> tiledbsoma::SOMACollectionBase -> SOMAExperiment

Active bindings

obs

a SOMADataFrame containing primary annotations on the observation axis. The contents of the soma_joinid column define the observation index domain, obs_id. All observations for the SOMAExperiment must be defined in this dataframe.

ms

a SOMACollection of named SOMAMeasurements.

Methods

Public methods

Inherited methods

Method axis_query()

Subset and extract data from a SOMAMeasurement by querying the obs/var axes.

Usage
SOMAExperiment$axis_query(measurement_name, obs_query = NULL, var_query = NULL)
Arguments
measurement_name

The name of the measurement to query.

obs_query, var_query

An SOMAAxisQuery object for the obs/var axis.

Returns

A SOMAExperimentAxisQuery object.

Method clone()

The objects of this class are cloneable with this method.

Usage
SOMAExperiment$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

SOMAExperiment Axis Query

Description

Perform an axis-based query against a SOMAExperiment.

SOMAExperimentAxisQuery allows easy selection and extraction of data from a single SOMAMeasurement in a SOMAExperiment, by obs/var (axis) coordinates and/or value filter. The primary use for this class is slicing SOMAExperiment X layers by obs or var value and/or coordinates. (lifecycle: experimental)

X Layer Support

Slicing on SOMASparseNDArray X matrices is supported; slicing on SOMADenseNDArray is not supported at this time.

Result Size

SOMAExperimentAxisQuery query class assumes it can store the full result of both axis dataframe queries in memory, and only provides incremental access to the underlying X NDArray. Accessors such as n_obs and n_vars codify this in the class.

Active bindings

experiment

The parent SOMAExperiment object.

indexer

The SOMAAxisIndexer object.

obs_query

The obs SOMAAxisQuery object.

var_query

The var SOMAAxisQuery object.

n_obs

The number of obs axis query results.

n_vars

The number of var axis query results.

obs_df

The obs SOMADataFrame object.

var_df

The var SOMADataFrame object for the specified measurement_name.

ms

The SOMAMeasurement object for the specified measurement_name.

Methods

Public methods

Method new()

Create a new SOMAExperimentAxisQuery object.

Usage
SOMAExperimentAxisQuery$new(
  experiment,
  measurement_name,
  obs_query = NULL,
  var_query = NULL
)
Arguments
experiment

A SOMAExperiment object.

measurement_name

The name of the measurement to query.

obs_query, var_query

An SOMAAxisQuery object for the obs/var axis.

Method obs()

Retrieve obs TableReadIter

Usage
SOMAExperimentAxisQuery$obs(column_names = NULL)
Arguments
column_names

A character vector of column names to retrieve

Method var()

Retrieve var arrow::Table

Usage
SOMAExperimentAxisQuery$var(column_names = NULL)
Arguments
column_names

A character vector of column names to retrieve

Method obs_joinids()

Retrieve soma_joinids as an arrow::Array for obs.

Usage
SOMAExperimentAxisQuery$obs_joinids()

Method var_joinids()

Retrieve soma_joinids as an arrow::Array for var.

Usage
SOMAExperimentAxisQuery$var_joinids()

Method X()

Retrieves an X layer as a linkSOMASparseNDArrayRead

Usage
SOMAExperimentAxisQuery$X(layer_name)
Arguments
layer_name

The name of the layer to retrieve.

Method read()

Reads the entire query result as a list of arrow::Tables. This is a low-level routine intended to be used by loaders for other in-core formats, such as Seurat, which can be created from the resulting Tables.

Usage
SOMAExperimentAxisQuery$read(
  X_layers = NULL,
  obs_column_names = NULL,
  var_column_names = NULL
)
Arguments
X_layers

The name(s) of the X layer(s) to read and return.

obs_column_names, var_column_names

Specify which column names in var and obs dataframes to read and return.

Method to_sparse_matrix()

Retrieve a collection layer as a sparse matrix with named dimensions.

Load any layer from the X, obsm, varm, obsp, or varp collections as a sparse matrix.

By default the matrix dimensions are named using the soma_joinid values in the specified layer's dimensions (e.g., soma_dim_0). However, dimensions can be named using values from any obs or var column that uniquely identifies each record by specifying the obs_index and var_index arguments.

For layers in obsm or varm, the column axis (the axis not indexed by “obs” or “var”) is set to the range of values present in “soma_dim_1”; this ensures that gaps in this axis are preserved (eg. when a query for “obs” that results in selecting entries that are all zero for a given PC)

Usage
SOMAExperimentAxisQuery$to_sparse_matrix(
  collection,
  layer_name,
  obs_index = NULL,
  var_index = NULL
)
Arguments
collection

The SOMACollection containing the layer of interest, either: "X", "obsm", "varm", "obsp", or "varp".

layer_name

Name of the layer to retrieve from the collection.

obs_index, var_index

Name of the column in obs or var (var_index) containing values that should be used as dimension labels in the resulting matrix. Whether the values are used as row or column labels depends on the selected collection:

Collection obs_index var_index
X row names column names
obsm row names ignored
varm ignored row names
obsp row and column names ignored
varp ignored row and column names
Returns

A Matrix::sparseMatrix

Method to_seurat()

Loads the query as a Seurat object

Usage
SOMAExperimentAxisQuery$to_seurat(
  X_layers = c(counts = "counts", data = "logcounts"),
  obs_index = NULL,
  var_index = NULL,
  obs_column_names = NULL,
  var_column_names = NULL,
  obsm_layers = NULL,
  varm_layers = NULL,
  obsp_layers = NULL
)
Arguments
X_layers

A named character of X layers to add to the Seurat assay where the names are the names of Seurat slots and the values are the names of layers within X; names should be one of:

  • “counts” to add the layer as counts

  • “data” to add the layer as data

  • “scale.data” to add the layer as scale.data

At least one of “counts” or “data” is required

obs_index

Name of column in obs to add as cell names; uses paste0("cell", obs_joinids()) by default

var_index

Name of column in var to add as feature names; uses paste0("feature", var_joinids()) by default

obs_column_names

Names of columns in obs to add as cell-level meta data; by default, loads all columns

var_column_names

Names of columns in var to add as feature-level meta data; by default, loads all columns

obsm_layers

Names of arrays in obsm to add as the cell embeddings; pass FALSE to suppress loading in any dimensional reductions; by default, loads all dimensional reduction information

varm_layers

Named vector of arrays in varm to load in as the feature loadings; names must be names of arrays in obsm (eg. varm_layers = c(X_pca = "PCs")); pass FALSE to suppress loading in any feature loadings; will try to determine varm_layers from obsm_layers

obsp_layers

Names of arrays in obsp to load in as Graphs; by default, loads all graphs

Returns

A Seurat object

Method to_seurat_assay()

Loads the query as a Seurat Assay

Usage
SOMAExperimentAxisQuery$to_seurat_assay(
  X_layers = c(counts = "counts", data = "logcounts"),
  obs_index = NULL,
  var_index = NULL,
  var_column_names = NULL
)
Arguments
X_layers

A named character of X layers to add to the Seurat assay where the names are the names of Seurat slots and the values are the names of layers within X; names should be one of:

  • “counts” to add the layer as counts

  • “data” to add the layer as data

  • “scale.data” to add the layer as scale.data

At least one of “counts” or “data” is required

obs_index

Name of column in obs to add as cell names; uses paste0("cell", obs_joinids()) by default

var_index

Name of column in var to add as feature names; uses paste0("feature", var_joinids()) by default

var_column_names

Names of columns in var to add as feature-level meta data; by default, loads all columns

Returns

An Assay object

Method to_seurat_reduction()

Loads the query as a Seurat dimensional reduction

Usage
SOMAExperimentAxisQuery$to_seurat_reduction(
  obsm_layer,
  varm_layer = NULL,
  obs_index = NULL,
  var_index = NULL
)
Arguments
obsm_layer

Name of array in obsm to load as the cell embeddings

varm_layer

Name of the array in varm to load as the feature loadings; by default, will try to determine varm_layer from obsm_layer

obs_index

Name of column in obs to add as cell names; uses paste0("cell", obs_joinids()) by default

var_index

Name of column in var to add as feature names; uses paste0("feature", var_joinids()) by default

Returns

A DimReduc object

Method to_seurat_graph()

Loads the query as a Seurat graph

Usage
SOMAExperimentAxisQuery$to_seurat_graph(obsp_layer, obs_index = NULL)
Arguments
obsp_layer

Name of array in obsp to load as the graph

obs_index

Name of column in obs to add as cell names; uses paste0("cell", obs_joinids()) by default

Returns

A Graph object

Method to_single_cell_experiment()

Loads the query as a SingleCellExperiment object

Usage
SOMAExperimentAxisQuery$to_single_cell_experiment(
  X_layers = NULL,
  obs_index = NULL,
  var_index = NULL,
  obs_column_names = NULL,
  var_column_names = NULL,
  obsm_layers = NULL,
  obsp_layers = NULL,
  varp_layers = NULL
)
Arguments
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_index

Name of column in obs to add as cell names; uses paste0("cell", obs_joinids()) by default

var_index

Name of column in var to add as feature names; uses paste0("feature", var_joinids()) by default

obs_column_names

Names of columns in obs to add as colData; by default, loads all columns

var_column_names

Names of columns in var to add as rowData; by default, loads all columns

obsm_layers

Names of arrays in obsm to add as the reduced dimensions; pass FALSE to suppress loading in any reduced dimensions; by default, loads all reduced dimensions

obsp_layers

Names of arrays in obsp to load in as SelfHits; by default, loads all graphs

varp_layers

Names of arrays in varp to load in as SelfHits; by default, loads all networks

Returns

A SingleCellExperiment object

Method clone()

The objects of this class are cloneable with this method.

Usage
SOMAExperimentAxisQuery$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Create SOMA Experiment

Description

Factory function to create a SOMADataFrame for writing, (lifecycle: experimental)

Usage

SOMAExperimentCreate(
  uri,
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp

Open SOMA Experiment

Description

Factory function to open a SOMAExperiment for reading, (lifecycle: experimental)

Usage

SOMAExperimentOpen(
  uri,
  mode = "READ",
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
mode

One of "READ" or "WRITE"
platform_config

Optional platform configuration
tiledbsoma_ctx

optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp. In READ mode, defaults to the current time. If non-NULL, then all members accessed through the collection object inherit the timestamp.

SOMA Measurement

Description

A SOMAMeasurement is a sub-element of a SOMAExperiment, and is otherwise a specialized SOMACollection with pre-defined fields: X, var, obsm/varm, and obsp/varp (see Active Bindings below for details). (lifecycle: experimental)

Adding new objects to a collection

The SOMAMeasurement class provides a number of type-specific methods for adding new a object to the collection, such as add_new_sparse_ndarray() and add_new_dataframe(). These methods will create the new object and add it as member of the SOMAMeasurement. The new object will always inherit the parent context (see SOMATileDBContext) and, by default, its platform configuration (see PlatformConfig). However, the user can override the default platform configuration by passing a custom configuration to the platform_config argument.

Super classes

tiledbsoma::TileDBObject -> tiledbsoma::TileDBGroup -> tiledbsoma::SOMACollectionBase -> SOMAMeasurement

Active bindings

var

a SOMADataFrame containing primary annotations on the variable axis, for variables in this measurement (i.e., annotates columns of X). The contents of the soma_joinid column define the variable index domain, var_id. All variables for this measurement must be defined in this dataframe.

X

a SOMACollection of SOMASparseNDArrays, each contains measured feature values indexed by ⁠[obsid, varid]⁠.

obsm

a SOMACollection of SOMADenseNDArrays containing annotations on the observation axis. Each array is indexed by obsid and has the same shape as obs.

obsp

a SOMACollection of SOMASparseNDArrays containing pairwise annotations on the observation axis and indexed with ⁠[obsid_1, obsid_2]⁠.

varm

a SOMACollection of SOMADenseNDArrays containing annotations on the variable axis. Each array is indexed by varid and has the same shape as var.

varp

a SOMACollection of SOMASparseNDArrays containing pairwise annotations on the variable axis and indexed with ⁠[varid_1, varid_2]⁠.

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
SOMAMeasurement$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Create SOMA Measurement

Description

Factory function to create a SOMAMeasurement for writing, (lifecycle: experimental)

Usage

SOMAMeasurementCreate(
  uri,
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp

Open SOMA Measurement

Description

Factory function to open a SOMAMeasurement for reading, (lifecycle: experimental)

Usage

SOMAMeasurementOpen(
  uri,
  mode = "READ",
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
mode

One of "READ" or "WRITE"
platform_config

Optional platform configuration
tiledbsoma_ctx

optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp. In READ mode, defaults to the current time. If non-NULL, then all members accessed through the collection object inherit the timestamp.

Open a SOMA Object

Description

Utility function to open the corresponding SOMA Object given a URI, (lifecycle: experimental)

Usage

SOMAOpen(
  uri,
  mode = "READ",
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
mode

One of "READ" or "WRITE"
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) with TileDB timestamp. For SOMACollections, all accessed members inherit the collection opening timestamp, and in READ mode the collection timestamp defaults to the time of opening.

SOMASparseNDArray

Description

SOMASparseNDArray is a sparse, N-dimensional array with offset (zero-based) integer indexing on each dimension. The SOMASparseNDArray has a user-defined schema, which includes:

  • type - a primitive type, expressed as an Arrow type (e.g., int64, float32, etc)

  • shape - the shape of the array, i.e., number and length of each dimension

All dimensions must have a positive, non-zero length.

Note - on TileDB this is an sparse array with N int64 dimensions of domain [0, maxInt64), and a single attribute.

Duplicate writes

As duplicate index values are not allowed, index values already present in the object are overwritten and new index values are added. (lifecycle: experimental)

Super classes

tiledbsoma::TileDBObject -> tiledbsoma::TileDBArray -> tiledbsoma::SOMAArrayBase -> tiledbsoma::SOMANDArrayBase -> SOMASparseNDArray

Methods

Public methods

Inherited methods

Method read()

Reads a user-defined slice of the SOMASparseNDArray

Usage
SOMASparseNDArray$read(
  coords = NULL,
  result_order = "auto",
  log_level = "auto"
)
Arguments
coords

Optional list of integer vectors, one for each dimension, with a length equal to the number of values to read. If NULL, all values are read. List elements can be named when specifying a subset of dimensions.

result_order

Optional order of read results. This can be one of either ⁠"ROW_MAJOR, ⁠"COL_MAJOR"⁠, or ⁠"auto"' (default).

log_level

Optional logging level with default value of "warn".

iterated

Option boolean indicated whether data is read in call (when FALSE, the default value) or in several iterated steps.

Returns

SOMASparseNDArrayRead

Method write()

Write matrix-like data to the array. (lifecycle: experimental)

Usage
SOMASparseNDArray$write(values)
Arguments
values

Any matrix-like object coercible to a TsparseMatrix. Character dimension names are ignored because SOMANDArray's use integer indexing.

Method nnz()

Retrieve number of non-zero elements (lifecycle: experimental)

Usage
SOMASparseNDArray$nnz()
Returns

A scalar with the number of non-zero elements

Method clone()

The objects of this class are cloneable with this method.

Usage
SOMASparseNDArray$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Create SOMA Sparse Nd Array

Description

Factory function to create a SOMASparseNDArray for writing, (lifecycle: experimental)

Usage

SOMASparseNDArrayCreate(
  uri,
  type,
  shape,
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
type

An Arrow type defining the type of each element in the array.
shape

A vector of integers defining the shape of the array.
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp

Open SOMA Sparse Nd Array

Description

Factory function to open a SOMASparseNDArray for reading, (lifecycle: experimental)

Usage

SOMASparseNDArrayOpen(
  uri,
  mode = "READ",
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL
)

Arguments

uri

URI for the TileDB object
mode

One of "READ" or "WRITE"
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext
tiledb_timestamp

Optional Datetime (POSIXct) for TileDB timestamp

SOMA TileDB Context

Description

Context map for TileDB-backed SOMA objects

Super classes

tiledbsoma::MappingBase -> tiledbsoma::ScalarMap -> tiledbsoma::SOMAContextBase -> SOMATileDBContext

Methods

Public methods

Inherited methods

Method new()

Usage
SOMATileDBContext$new(config = NULL, cached = TRUE)
Arguments
config

...

cached

Force new creation

Returns

An instantiated SOMATileDBContext object

Method keys()

Usage
SOMATileDBContext$keys()
Returns

The keys of the map

Method items()

Usage
SOMATileDBContext$items()
Returns

Return the items of the map as a list

Method length()

Usage
SOMATileDBContext$length()
Returns

The number of items in the map

Method get()

Usage
SOMATileDBContext$get(key, default = quote(expr = ))
Arguments
key

Key to fetch

default

Default value to fetch if key is not found; defaults to NULL

Returns

The value of key in the map, or default if key is not found

Method set()

Usage
SOMATileDBContext$set(key, value)
Arguments
key

Key to set

value

Value to add for key, or NULL to remove the entry for key

Returns

[chainable] Invisibly returns self with value added as key

Method to_tiledb_context()

Usage
SOMATileDBContext$to_tiledb_context()
Returns

A tiledb_ctx object, dynamically constructed. Most useful for the constructor of this class.

Method context()

Usage
SOMATileDBContext$context()
Returns

A tiledb_ctx object, which is a stored (and long-lived) result from to_tiledb_context.

Method clone()

The objects of this class are cloneable with this method.

Usage
SOMATileDBContext$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

SparseReadIter

Description

SparseReadIter is a class that allows for iteration over a reads on SOMASparseNDArray. Iteration chunks are retrieved as 0-based Views matrixZeroBasedView of Matrix::sparseMatrix.

Super class

tiledbsoma::ReadIter -> SparseReadIter

Methods

Public methods

Inherited methods

Method new()

Create (lifecycle: experimental)

Usage
SparseReadIter$new(sr, shape, zero_based = FALSE)
Arguments
sr

Soma reader pointer

shape

Shape of the full matrix

zero_based

Logical, if TRUE will make iterator for Matrix::dgTMatrix-class otherwise matrixZeroBasedView.

Method concat()

Concatenate remainder of iterator.

Usage
SparseReadIter$concat()
Returns

matrixZeroBasedView of Matrix::sparseMatrix

Method clone()

The objects of this class are cloneable with this method.

Usage
SparseReadIter$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

SOMA Read Iterator over Arrow Table

Description

TableReadIter is a class that allows for iteration over a reads on SOMASparseNDArray and SOMADataFrame. Iteration chunks are retrieved as arrow::Table

Super class

tiledbsoma::ReadIter -> TableReadIter

Methods

Public methods

Inherited methods

Method concat()

Concatenate remainder of iterator.

Usage
TableReadIter$concat()
Returns

arrow::Table

Method clone()

The objects of this class are cloneable with this method.

Usage
TableReadIter$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

TileDB Object Base Class

Description

Base class to implement shared functionality across the TileDBArray and TileDBGroup classes. (lifecycle: experimental)

Active bindings

platform_config

Platform configuration

tiledbsoma_ctx

SOMATileDBContext

uri

The URI of the TileDB object.

Methods

Public methods

Method new()

Create a new TileDB object. (lifecycle: experimental)

Usage
TileDBObject$new(
  uri,
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL,
  internal_use_only = NULL
)
Arguments
uri

URI for the TileDB object

platform_config

Optional platform configuration

tiledbsoma_ctx

Optional SOMATileDBContext

tiledb_timestamp

Optional Datetime (POSIXct) with TileDB timestamp

internal_use_only

Character value to signal this is a 'permitted' call, as new() is considered internal and should not be called directly.

Method class()

Print the name of the R6 class.

Usage
TileDBObject$class()

Method is_open()

Determine if the object is open for reading or writing

Usage
TileDBObject$is_open()
Returns

TRUE if the object is open, otherwise FALSE

Method mode()

Get the mode of the object

Usage
TileDBObject$mode()
Returns

If the object is closed, returns “CLOSED”; otherwise returns the mode (eg. “READ”) of the object

Method print()

Print-friendly representation of the object.

Usage
TileDBObject$print()

Method exists()

Check if the object exists. (lifecycle: experimental)

Usage
TileDBObject$exists()
Returns

⁠TRUE`` if the object exists, ⁠FALSE' otherwise.

Method clone()

The objects of this class are cloneable with this method.

Usage
TileDBObject$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

TileDB SOMA statistics

Description

These functions expose the TileDB Core functionality for performance measurements and statistics.

Usage

tiledbsoma_stats_enable()

tiledbsoma_stats_disable()

tiledbsoma_stats_reset()

tiledbsoma_stats_dump()

tiledbsoma_stats_show()

Details

  • tiledbsoma_stats_enable()/tiledbsoma_stats_disable(): Enable and disable TileDB's internal statistics.

  • tiledbsoma_stats_reset(): Reset all statistics to 0.

  • tiledbsoma_stats_dump(): Dump all statistics to a JSON string.

  • tiledbsoma_stats_show(): Print all statistics to the console.

Write a SOMA Object from an R Object

Description

Convert R objects to their appropriate SOMA counterpart function and methods can be written for it to provide a high-level R →\rightarrow SOMA interface

Usage

write_soma(x, uri, ..., platform_config = NULL, tiledbsoma_ctx = NULL)

Arguments

x

An object
uri

URI for resulting SOMA object
...

Arguments passed to other methods
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext

Value

The URI to the resulting SOMAExperiment generated from the data contained in x, returned opened for write

Known methods

Write a Seurat object to a SOMA, returned opened for write

Description

Write a Seurat object to a SOMA, returned opened for write

Usage

## S3 method for class 'Seurat'
write_soma(x, uri, ..., platform_config = NULL, tiledbsoma_ctx = NULL)

Arguments

x

A Seurat object
uri

URI for resulting SOMA object
...

Arguments passed to other methods
platform_config

Optional platform configuration
tiledbsoma_ctx

Optional SOMATileDBContext

Value

The URI to the resulting SOMAExperiment generated from the data contained in x, returned opened for write

Writing Cell-Level Meta Data

Cell-level meta data is written out as a data frame called “obs” at the experiment level

Writing Assays

Seurat Assay objects are written out as individual measurements:

  • the “data” matrix is written out a sparse matrix called “data” within the “X” group

  • the “counts” matrix, if not empty, is written out a sparse matrix called “counts” within the “X” group

  • the “scale.data” matrix, if not empty, is written out a sparse matrix called “scale_data” within the “X” group

  • feature-level meta data is written out as a data frame called “var”

Expression matrices are transposed (cells as rows) prior to writing. All other slots, including results from extended assays (eg. SCTAssay, ChromatinAssay) are lost

Writing DimReducs

Seurat DimReduc objects are written out to the “obsm” and “varm” groups of a measurement:

  • cell embeddings are written out as a sparse matrix in the “obsm” group

  • feature loadings, if not empty, are written out as a sparse matrix in the “varm” groups; loadings are padded with NAs to include all features

Dimensional reduction names are translated to AnnData-style names (eg. “pca” becomes X_pca for embeddings and “PCs” for loadings). All other slots, including projected feature loadings and jackstraw information, are lost

Writing Graphs

Seurat Graph objects are written out as sparse matrices to the “obsp” group of a measurement