fix the JoinLayers logic inside scVI.R

[longmanz]

This is a bug reported by multiple users (e.g., #209) and have been confirmed. This is caused by the fact that JoinLayers() does not support SCTAssay (SCTAssay is already a single matrix, so no need to join), so when performing scVI integration with SCT-corrected assay, users will run into error.

To reproduce this error, one can run

library(Seurat)
library(SeuratData)
library(SeuratWrappers)

#  SeuratData::InstallData("pbmcsca")
obj <- SeuratData::LoadData("pbmcsca")
obj <- UpdateSeuratObject(obj)

obj[["RNA"]] <- split(obj[["RNA"]], f = obj$Method)
obj <- SCTransform(object = obj)
obj <- RunPCA(obj)

obj <- IntegrateLayers(
    object = obj, method = scVIIntegration,
    orig.reduction = "pca", new.reduction = "integrated.scvi",
    assay = "SCT", conda_env = "/Users/uqljian5/opt/anaconda3/envs/scvi", verbose = FALSE
)

This PR proposes a fix which was originally from https://github.com/satijalab/project-management/issues/131. Basically, now when SCTAssay is used for scVI integration, the function will perform a check on the object type, and skip the JoinLayers() if it is SCTAssay.

[Copilot]

Pull request overview

Fixes scVI integration when using SCTransform by avoiding JoinLayers() on SCTAssay objects (which don’t implement JoinLayers() and are already represented as a single matrix), and by splitting batch labels via SCT model identifiers instead of layers.

Changes:

• Skip JoinLayers() when the input is an SCTAssay, preventing the reported JoinLayers.SCTAssay dispatch error.
• Refactor batch construction logic by separating SCT-specific batch detection into a new .FindSCTBatches() helper.
• Update internal roxygen describing how batches are computed (StdAssay-by-layer vs SCT-by-model).

Comments suppressed due to low confidence (1)

R/scVI.R:208

• There are multiple trailing blank lines at the end of the file after .FindSCTBatches(). Please remove the extra empty lines to keep file formatting consistent with the rest of the R sources in this repo.

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[anashen]

Thanks @longmanz for the reproducible example & fix! Tested + made some minor edits to function documentation.