Scaling and centering in FindIntegrationAnchors() with reduction = "rlsi"

[angelosarmen]

Hi,

In FindIntegrationAnchors() with reduction = "rlsi", ReciprocalProject() is called with do.center = TRUE and do.scale = FALSE , and these options are passed to ProjectSVD(). However, RunSVD() in Signac centers and scales the embeddings. Therefore, Embeddings(object = object.1[[reduction]]) and proj.2 would be centered but be on different scales (same for proj.1 and Embeddings(object = object.2[[reduction]]). Could you please explain why isn't scaling performed?

ReciprocalProject <- function(
  object.1,
  object.2,
  reduction,
  dims,
  projected.name,
  features,
  do.scale,
  do.center,
  slot,
  l2.norm,
  verbose = TRUE
) {
  common.features <- intersect(
    x = rownames(x = Loadings(object = object.1[[reduction]])),
    y = rownames(x = Loadings(object = object.2[[reduction]]))
  )
  common.features <- intersect(
    x = common.features,
    y = features
  )
  object.pair <- merge(x = object.1, y = object.2, merge.data = TRUE)
  data.1 <- GetAssayData(
    object = object.1,
    slot = slot
  )
  data.2 <- GetAssayData(
    object = object.2,
    slot = slot
  )

  proj.1 <- ProjectSVD(
    reduction = object.2[[reduction]],
    data = data.1,
    mode = reduction,
    features = common.features,
    do.scale = do.scale,
    do.center = do.center,
    use.original.stats = FALSE,
    verbose = verbose
  )
  proj.2 <- ProjectSVD(
    reduction = object.1[[reduction]],
    data = data.2,
    mode = reduction,
    features = common.features,
    do.scale = do.scale,
    do.center = do.center,
    use.original.stats = FALSE,
    verbose = verbose
  )
  # object.1 is ref, and object.2 is query
  reduction.dr.name.1 <- paste0(projected.name, ".ref")
  reduction.dr.name.2 <- paste0(projected.name, ".query")
  object.pair[[reduction.dr.name.1]] <- CreateDimReducObject(
    embeddings = rbind(Embeddings(object = object.1[[reduction]]), proj.2)[,dims],
    loadings = Loadings(object = object.1[[reduction]])[,dims],
    assay = DefaultAssay(object = object.1),
    key = paste0(projected.name, "ref_")
  )
  object.pair[[reduction.dr.name.2]] <- CreateDimReducObject(
    embeddings = rbind(proj.1, Embeddings(object = object.2[[reduction]]))[,dims],
    loadings = Loadings(object = object.2[[reduction]])[,dims],
    assay = DefaultAssay(object = object.2),
    key = paste0(projected.name, "query_")
  )
  object.pair[[reduction]] <- CreateDimReducObject(
    embeddings = rbind(
      Embeddings(object = object.1[[reduction]]),
      Embeddings(object = object.2[[reduction]]))[,dims],
    loadings = Loadings(object = object.1[[reduction]])[,dims],
    assay = DefaultAssay(object = object.1),
    key = paste0(projected.name, "_")
  )
  if (l2.norm) {
    slot(object = object.pair[[reduction.dr.name.1]], name = "cell.embeddings") <- Sweep(
      x = Embeddings(object = object.pair[[reduction.dr.name.1]]),
      MARGIN = 2,
      STATS = apply(X = Embeddings(object = object.pair[[reduction.dr.name.1]]), MARGIN = 2, FUN = sd),
      FUN = "/"
    )
    slot(object = object.pair[[reduction.dr.name.2]], name = "cell.embeddings") <- Sweep(
      x = Embeddings(object = object.pair[[reduction.dr.name.2]]),
      MARGIN = 2,
      STATS = apply(X = Embeddings(object = object.pair[[reduction.dr.name.2]]), MARGIN = 2, FUN = sd),
      FUN = "/"
    )

    object.pair <- L2Dim(object = object.pair, reduction = reduction.dr.name.1)
    object.pair <- L2Dim(object = object.pair, reduction = reduction.dr.name.2)
  }
  return(object.pair)
}

[dcollins15]

Thanks for using Seurat!

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