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