AzimuthBridgeReference: Create a Seurat object compatible with Azimuth.

In satijalab/azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data

Create a Seurat object compatible with Azimuth.

Description

Create a Seurat object compatible with Azimuth.

Usage

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.

satijalab/azimuth documentation built on Nov. 19, 2023, 8:34 a.m.