AzimuthReference | R Documentation |
Create a Seurat object compatible with Azimuth.
AzimuthReference(
object,
refUMAP = "umap",
refDR = "spca",
refAssay = "SCT",
dims = 1:50,
k.param = 31,
plotref = "umap",
plot.metadata = NULL,
ori.index = NULL,
colormap = NULL,
assays = NULL,
metadata = NULL,
reference.version = "0.0.0",
verbose = FALSE
)
object |
Seurat object |
refUMAP |
Name of UMAP in reference to use for mapping |
refDR |
Name of DimReduc in reference to use for mapping |
refAssay |
Name of SCTAssay to use in reference |
dims |
Dimensions to use in reference neighbor finding |
k.param |
Defines k for the k-nearest neighbor algorithm |
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 |
assays |
Assays to retain for transfer |
metadata |
Metadata to retain for transfer |
reference.version |
Version of the Azimuth reference |
verbose |
Display progress/messages |
Returns a Seurat object with AzimuthData stored in the tools slot for use with Azimuth.
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