build_vesalius_assay: build vesalius assay object

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

build vesalius assay object

Description

build a simple vesalius assay object from single count matrix and spatial coordinate pair.

Usage

build_vesalius_assay(
  coordinates,
  counts = NULL,
  image = NULL,
  assay = "spatial_omics",
  scale = "auto",
  unit = "um",
  verbose = TRUE
)

Arguments

coordinates	data.frame in the format barcodes, x, y. Default is NULL. See details.
counts	matrix, sparse matrix containing counts. Default is NULL. See details.
image	connection string or image array
assay	character vector containing names of the assays (see details).
scale	character | numeric - if "auto", vesalius will compute 99 percentile of inter barcodes distance else provide a numeric value describing distance between barcodes.
unit	character - units of scale
verbose	logical indicating if progress message should be outputed or not.

Details

The vesalius_assay constructor allows you to create partial or complete vesalius_assay objects.

Partial objects contain only the coordinates.

Complete objects contain both the counts and the coordinates.

The main purpose of using partial objects (or empty objects) is for you to be able to provide your own count matrix. This will be useful if you want to normalise your data in a way that is not provided by vesalius.

This approach of using your own data can also apply to embeddings. If you have generated a set of latent space embeddings that you wish to use instead of those provided by vesalius, you can use the add_embeddings function.

Along side this input data, you can provide a name to your assay. If none are provided, Vesalius will generate a set of names based on the default assay name "spatial_omics".

You can decide if you want to adjust the coordinates to the origin i.e remove unnecessary space or normalise the coordinates. Norm is not recommened at the moment

Value

A vesalius_assay objecy

Examples

data(vesalius)
# Single assay object
ves <- build_vesalius_assay(coordinates, counts)

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