Split up map to reference by samples for SeuratMap2Ref

[pwwang]

Seurat vignette (bottom of the page): https://satijalab.org/seurat/articles/multimodal_reference_mapping

query.batches <- SplitObject(query, split.by = "sampleid")
 
#query.batches <- lapply(X = query.batches, FUN = SCTransform, verbose = FALSE)              # from Seurat vignette
#modified version
for (i in 1:length(query.batches)) {
  print(i)
  query.batches[[i]] <- SCTransform(query.batches[[i]],
              assay="RNA",
              residual.features = rownames(x = reference),
              method = 'glmGamPoi',
              ncells = 4000,
              n_genes = 5000,
              vars.to.regress = "percent.mt",
              do.correct.umi = FALSE,
              do.scale = FALSE,
              do.center = TRUE,
                      verbose = FALSE)
}
 
anchors <- list()
for (i in 1:length(query.batches)) {
  anchors[[i]] <- FindTransferAnchors(
    reference = reference,
    query = query.batches[[i]],
    normalization.method = "SCT",
    #  recompute.residuals=FALSE,
    reference.reduction = "spca",
    k.filter = NA,
    dims = 1:15
    )
}
 
for (i in 1:length(query.batches)) {
  query.batches[[i]] <- MapQuery(
    anchorset = anchors[[i]],
    query = query.batches[[i]],
    reference = reference,
    refdata = list(
      celltype = "celltype.l2",
      predicted_ADT = "ADT"),
    reference.reduction = "spca",
    reduction.model = "wnn.umap"
  )
}
 
for (i in 1:length(query.batches)) {
  query.batches[[i]] <- AddMetaData(
    object = query.batches[[i]],
    metadata = MappingScore(anchors = anchors[[i]]),
    col.name = "mapping.score"
  )
}
 
# Merge the batches
query <- merge(query.batches[[1]], query.batches[2:length(query.batches)], merge.dr = "ref.umap")
query