AnnotationPairwiseMatrixGroup: Single-cell Annotation Matrix Group

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

Single-cell Annotation Matrix Group

Description

Class for representing a TileDB group containing one or more AnnotationPairwiseMatrix arrays that share a common dimension name.

Super classes

tiledbsc::TileDBObject -> tiledbsc::TileDBGroup -> tiledbsc::AnnotationGroup -> AnnotationPairwiseMatrixGroup

Methods

Public methods

• AnnotationPairwiseMatrixGroup$add_matrix()

• AnnotationPairwiseMatrixGroup$add_seurat_graph()

• AnnotationPairwiseMatrixGroup$clone()

Inherited methods

• tiledbsc::TileDBObject$class()
• tiledbsc::TileDBObject$exists()
• tiledbsc::TileDBGroup$add_member()
• tiledbsc::TileDBGroup$add_metadata()
• tiledbsc::TileDBGroup$count_members()
• tiledbsc::TileDBGroup$get_member()
• tiledbsc::TileDBGroup$get_members()
• tiledbsc::TileDBGroup$get_metadata()
• tiledbsc::TileDBGroup$group_exists()
• tiledbsc::TileDBGroup$list_member_uris()
• tiledbsc::TileDBGroup$list_members()
• tiledbsc::TileDBGroup$list_object_uris()
• tiledbsc::TileDBGroup$list_objects()
• tiledbsc::TileDBGroup$print()
• tiledbsc::TileDBGroup$remove_member()
• tiledbsc::TileDBGroup$tiledb_group()
• tiledbsc::AnnotationGroup$initialize()
• tiledbsc::AnnotationGroup$reset_query()
• tiledbsc::AnnotationGroup$set_query()

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Method add_matrix()

Add a new AnnotationPairwiseMatrix array to the group.

Usage

AnnotationPairwiseMatrixGroup$add_matrix(data, name, metadata = NULL)

Arguments

data

a matrix of annotation data to ingest. The matrix rows must be aligned to the dimension indicated by the group's dimension_name.

name

Name of the new pairwise annotation matrix.

metadata

Named list of metadata to add.

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Method add_seurat_graph()

Convert a SeuratObject::Graph object to AnnotationPairwiseMatrix.

Usage

AnnotationPairwiseMatrixGroup$add_seurat_graph(object, technique)

Arguments

object

A SeuratObject::Graph object.

technique

Name of the technique used to generate the graph (typically, nn or snn).

Details

On-Disk Format

Arrays are named ⁠graph_<technique>⁠.

Metadata

• assay_used: Name of the assay used to generate the graph.

• graph_technique: Name of the technique used to generate the graph. used.

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Method clone()

The objects of this class are cloneable with this method.

Usage

AnnotationPairwiseMatrixGroup$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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