Coerce a single-cell object into a CoPro object

One-call coercion from SingleCellExperiment or Seurat objects into CoProSingle (asCoProSingle()) or CoProMulti (asCoProMulti()) objects. These helpers extract the relevant expression matrix, spatial coordinates, cell metadata, and cell-type labels, then delegate to newCoProSingle() / newCoProMulti() so all validation stays single-sourced.

Usage

asCoProSingle(
  x,
  spatialDim = "spatial",
  cellTypeCol,
  assay = NULL,
  layer = "data",
  ...
)

asCoProMulti(
  x,
  spatialDim = "spatial",
  cellTypeCol,
  slideCol = NULL,
  assay = NULL,
  layer = "data",
  ...
)

# S4 method for class 'ANY'
asCoProSingle(
  x,
  spatialDim = "spatial",
  cellTypeCol,
  assay = NULL,
  layer = "data",
  ...
)

# S4 method for class 'ANY'
asCoProMulti(
  x,
  spatialDim = "spatial",
  cellTypeCol,
  slideCol = NULL,
  assay = NULL,
  layer = "data",
  ...
)

Arguments

x: A SingleCellExperiment or Seurat object.
spatialDim: Name of the reducedDim / image / reduction that holds 2-D (or 3-D) spatial coordinates. Default "spatial".
cellTypeCol: Name of the column in the object's cell-level metadata that holds cell type labels. Required.
assay: Optional assay name. For SingleCellExperiment defaults to "logcounts" when available, otherwise the first assay. For Seurat defaults to SeuratObject::DefaultAssay(x).
layer: Seurat-only. Layer (formerly "slot") to pull expression data from. Default "data".
...: Additional arguments passed through to newCoProSingle() / newCoProMulti() (for example for future extensions).
slideCol: (asCoProMulti() only) Name of the column in the object's cell-level metadata that holds the slide/sample identifier.

Value

A CoProSingle or CoProMulti object.

Details

For SingleCellExperiment objects:

normalizedData comes from SummarizedExperiment::assay(x, assay) (default "logcounts" if present, else the first assay), transposed into cells-by-genes orientation.
locationData comes from SingleCellExperiment::reducedDim(x, spatialDim) (expected to have 2 or 3 columns renamed to x, y, optionally z).
metaData comes from SummarizedExperiment::colData(x) as a data.frame.
cellTypes comes from the column of colData(x) named cellTypeCol.

For Seurat objects:

normalizedData comes from SeuratObject::GetAssayData(x, layer = layer, assay = assay), transposed into cells-by-genes orientation.
locationData comes from either x[[spatialDim]]@coordinates (when spatialDim refers to a spatial image/slice) or SeuratObject::Embeddings(x, reduction = spatialDim) (when it refers to a dimensionality reduction).
metaData comes from the object's [[]] slot.
cellTypes comes from x[[cellTypeCol]][, 1].

Both conversions require the corresponding package to be installed (SingleCellExperiment / SummarizedExperiment or SeuratObject) and will error with an install hint otherwise.

Examples

toy <- readRDS(
  system.file("extdata", "toy_copro_data.rds", package = "CoPro")
)

## --- From a SingleCellExperiment -----------------------------------------
if (requireNamespace("SingleCellExperiment", quietly = TRUE) &&
    requireNamespace("SummarizedExperiment", quietly = TRUE) &&
    requireNamespace("S4Vectors", quietly = TRUE)) {
  sce <- SingleCellExperiment::SingleCellExperiment(
    assays = list(logcounts = t(toy$normalizedData))
  )
  SummarizedExperiment::colData(sce) <- S4Vectors::DataFrame(
    toy$metaData, cellType = toy$cellTypes
  )
  SingleCellExperiment::reducedDim(sce, "spatial") <-
    as.matrix(toy$locationData)
  obj_sce <- asCoProSingle(
    sce, spatialDim = "spatial", cellTypeCol = "cellType"
  )
}

## --- From a Seurat object -----------------------------------------------
if (requireNamespace("SeuratObject", quietly = TRUE)) {
  expr_gbc <- t(toy$normalizedData)  # genes x cells
  srt <- SeuratObject::CreateSeuratObject(
    counts = expr_gbc, min.cells = 0, min.features = 0
  )
  srt <- SeuratObject::SetAssayData(
    srt, layer = "data", new.data = expr_gbc
  )
  srt[["cellType"]] <- toy$cellTypes
  coords <- as.matrix(toy$locationData)
  rownames(coords) <- colnames(srt)
  colnames(coords) <- c("spatial_1", "spatial_2")
  srt[["spatial"]] <- SeuratObject::CreateDimReducObject(
    embeddings = coords, key = "spatial_", assay = "RNA"
  )
  obj_srt <- asCoProSingle(
    srt, spatialDim = "spatial", cellTypeCol = "cellType"
  )
}