SOMAExperiment Axis Query

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: maturing)

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

• SOMAExperimentAxisQuery$new()

• SOMAExperimentAxisQuery$obs()

• SOMAExperimentAxisQuery$var()

• SOMAExperimentAxisQuery$obs_joinids()

• SOMAExperimentAxisQuery$var_joinids()

• SOMAExperimentAxisQuery$X()

• SOMAExperimentAxisQuery$obsm()

• SOMAExperimentAxisQuery$varm()

• SOMAExperimentAxisQuery$obsp()

• SOMAExperimentAxisQuery$varp()

• SOMAExperimentAxisQuery$read()

• SOMAExperimentAxisQuery$to_sparse_matrix()

• SOMAExperimentAxisQuery$to_seurat()

• SOMAExperimentAxisQuery$to_seurat_assay()

• SOMAExperimentAxisQuery$to_seurat_reduction()

• SOMAExperimentAxisQuery$to_seurat_graph()

• SOMAExperimentAxisQuery$to_single_cell_experiment()

• SOMAExperimentAxisQuery$clone()

---

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 SOMASparseNDArrayRead

Usage

SOMAExperimentAxisQuery$X(layer_name)

Arguments

layer_name

The name of the layer to retrieve.

---

Method obsm()

Retrieves an obsm layer as a SOMASparseNDArrayRead

Usage

SOMAExperimentAxisQuery$obsm(layer_name)

Arguments

layer_name

The name of the layer to retrieve

---

Method varm()

Retrieves a varm layer as a SOMASparseNDArrayRead

Usage

SOMAExperimentAxisQuery$varm(layer_name)

Arguments

layer_name

The name of the layer to retrieve

---

Method obsp()

Retrieves an obsp layer as a SOMASparseNDArrayRead

Usage

SOMAExperimentAxisQuery$obsp(layer_name)

Arguments

layer_name

The name of the layer to retrieve

---

Method varp()

Retrieves a varp layer as a SOMASparseNDArrayRead

Usage

SOMAExperimentAxisQuery$varp(layer_name)

Arguments

layer_name

The name of the layer to retrieve

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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,
  drop_levels = FALSE
)

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

drop_levels

Drop unused levels from obs and var factor columns

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,
  drop_levels = FALSE
)

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

drop_levels

Drop unused levels from var factor 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,
  drop_levels = FALSE
)

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

drop_levels

Drop unused levels from obs and var factor columns

Returns

A SingleCellExperiment object

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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.