AnnotationPairwiseMatrix: Single-cell Annotation Pairwise Matrix

In TileDB-Inc/tiledbsc: TileDB Single Cell SOMA API

Single-cell Annotation Pairwise Matrix

Description

Single-cell Annotation Pairwise Matrix

Single-cell Annotation Pairwise Matrix

Details

Base class for matrix-like data storing pairwise relationships with rows and columns aligned to either the observations or features of X (AssayMatrix).

Super classes

tiledbsc::TileDBObject -> tiledbsc::TileDBArray -> tiledbsc::AnnotationArray -> AnnotationPairwiseMatrix

Methods

Public methods

• AnnotationPairwiseMatrix$from_matrix()

• AnnotationPairwiseMatrix$to_matrix()

• AnnotationPairwiseMatrix$to_dataframe()

• AnnotationPairwiseMatrix$to_sparse_matrix()

• AnnotationPairwiseMatrix$to_seurat_graph()

• AnnotationPairwiseMatrix$clone()

Inherited methods

• tiledbsc::TileDBObject$class()
• tiledbsc::TileDBObject$exists()
• tiledbsc::TileDBArray$add_metadata()
• tiledbsc::TileDBArray$array_exists()
• tiledbsc::TileDBArray$attributes()
• tiledbsc::TileDBArray$attrnames()
• tiledbsc::TileDBArray$dimensions()
• tiledbsc::TileDBArray$dimnames()
• tiledbsc::TileDBArray$fragment_count()
• tiledbsc::TileDBArray$get_metadata()
• tiledbsc::TileDBArray$initialize()
• tiledbsc::TileDBArray$print()
• tiledbsc::TileDBArray$reset_query()
• tiledbsc::TileDBArray$schema()
• tiledbsc::TileDBArray$set_query()
• tiledbsc::TileDBArray$tiledb_array()

---

Method from_matrix()

Ingest annotation matrix

Usage

AnnotationPairwiseMatrix$from_matrix(x, index_cols, value_col = "value")

Arguments

x

any matrix-like object coercible to a TsparseMatrix with string dimensions.

index_cols

Names to use for the TileDB array's dimensions that will contain the matrix row/column names.

value_col

Name to use for the TileDB array's attribute that will contain the matrix values.

---

Method to_matrix()

Read annotation data from TileDB into a matrix

Usage

AnnotationPairwiseMatrix$to_matrix()

Returns

A matrix

---

Method to_dataframe()

Read annotation data from TileDB into a data frame

Usage

AnnotationPairwiseMatrix$to_dataframe(attrs = NULL)

Arguments

attrs

Specify one or more attributes to retrieve. If NULL, all attributes are retrieved.

Returns

A data.frame

---

Method to_sparse_matrix()

Read annotation data from TileDB into a sparse matrix

Usage

AnnotationPairwiseMatrix$to_sparse_matrix()

Returns

A Matrix::dgTMatrix.

---

Method to_seurat_graph()

Read annotation data from TileDB into Seurat Graph

Usage

AnnotationPairwiseMatrix$to_seurat_graph()

Returns

A SeuratObject::Graph

---

Method clone()

The objects of this class are cloneable with this method.

Usage

AnnotationPairwiseMatrix$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

TileDB-Inc/tiledbsc documentation built on Aug. 26, 2023, 2:32 p.m.