integrate_assays: integrate 2 vesalius assays

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

integrate 2 vesalius assays

Description

integrate 2 vesalius assays

Usage

integrate_assays(
  mapped,
  reference,
  method = "CCAIntegration",
  nfeatures = 2000,
  signal = "variable_features",
  dimensions = 30,
  infer = TRUE,
  use_counts = "raw",
  labels_mapped = NULL,
  labels_reference = NULL,
  regenerate_tiles = TRUE,
  tensor_resolution = 1,
  filter_grid = 1,
  filter_threshold = 1,
  verbose = TRUE
)

Arguments

mapped	vesalius_assay object - mapped veslius assay (map_assays)
reference	vesalius_assay object - reference vesalius_assay (seed)
method	character - count integration method (methods provided by Seurat v5)
nfeatures	integer - number of variable features to sue during integration.
signal	character - defining which signal should be returned: variable_features, all_features or custom gene list.
dimensions	interger - number of dimensions integrated latent space dimensions.
infer	logical - back infer original counts by reversing reduced dimensional space roations.
use_counts	character - which count matrix to use during integration
labels_mapped	character - which columns in the mapped data assay should be merged with the reference data (see details)
labels_reference	character - which columns in the reference data assay should be merged with the mapped data (see details)
regenerate_tiles	logical - should tiles be regenrated from integrated coordinates
verbose	logical - should progressed message be printed

Details

After mapping coordinates from a query onto a reference, vesalius provides a way to then integrate the assays together. This function will:

* Integrate Counts using Seurat * Merge coordinates (adding a jitter to avoid overlapping coordinayes) * Merge territories (pair-wise merging using labels_mapped and labels_reference - everything else will have a separate column).

We also infer log nomalized counts from CCA latent space.

The final output of this function is a vesalius_assay object containing coordinates from the mapped and reference, integrated latent space (e.g.CCA) integrated counts, merged territories, an additional meta data.

It should be noted that this object does not contain tiles. To use this vesalius_assay as any other, add tiles by using generate_tiles

Value

a vesalius_assay object

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