add_embeddings: Add embeddings Add custom embeddings to vesalius objects

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

Add embeddings Add custom embeddings to vesalius objects

Description

Add embeddings Add custom embeddings to vesalius objects

Usage

add_embeddings(vesalius_assay, embeddings, add_name = NULL, verbose = TRUE)

Arguments

vesalius_assay	a vesalius_assay object
embeddings	a matrix containing embedding values (see details)
add_name	character string to be used as embedding name.
verbose	logical indicating if progress message should be outputed.

Details

Vesalius objects accepts custom embedding values that will be used to generate images.

The embedding matrix should be in the form of a matrix with columns being the latent space dimensiions and rows representing the spatial indices present in the data set.

The intersection between spatial indices present in the tiles and custom embeddings will be used. This intersection will be applied to the custom embeddings and filter out all tiles that are not present in the tiles. The tiles will not be filtered.

Rownames should also be present and should represent the barcode name. These rownames are use to match the latent space embedding to its tile in the image.

Value

a vesalius_assay object

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.