Create a Seurat object compatible with Azimuth.

AzimuthBridgeReference(
  object,
  reference.reduction = "spca",
  bridge.ref.reduction = "ref.spca",
  bridge.query.reduction = "slsi",
  laplacian.reduction = "lap",
  refUMAP = "wnn.umap",
  refAssay = "SCT",
  dims = 1:50,
  plotref = "wnn.umap",
  plot.metadata = NULL,
  ori.index = NULL,
  colormap = NULL,
  assays = c("Bridge", "RNA"),
  metadata = NULL,
  reference.version = "0.0.0",
  verbose = FALSE
)

Arguments

object: Seurat object
refUMAP: Name of UMAP in reference to use for mapping
refAssay: Name of SCTAssay to use in reference
dims: Dimensions to use in reference neighbor finding
plotref: Either the name of the DimReduc in the provided Seurat object to use for the plotting reference or the DimReduc object itself.
plot.metadata: A data.frame of discrete metadata fields for the cells in the plotref.
ori.index: Index of the cells used in mapping in the original object on which UMAP was run. Only need to provide if UMAP was run on different set of cells.
colormap: A list of named and ordered vectors specifying the colors and levels for the metadata. See CreateColorMap for help generating your own.
assays: Assays to retain for transfer
metadata: Metadata to retain for transfer
reference.version: Version of the Azimuth reference
verbose: Display progress/messages
refDR: Name of DimReduc in reference to use for mapping
k.param: Defines k for the k-nearest neighbor algorithm

Value

Returns a Seurat object with AzimuthData stored in the tools slot for use with Azimuth.