Converts a SpaMTP Seurat object to a Cardinal object, including annotations and metadata

Usage

ConvertSeuratToCardinal(
  data,
  assay = "Spatial",
  slot = "counts",
  run_col = NULL,
  feature.metadata = FALSE,
  verbose = TRUE
)

Arguments

data: Seurat object being converted.
assay: Character string defining the Seurat Object assay name to pull intensity count data from (default = "Spatial").
slot: Character string defining which slot from the Seurat Object assay to gather intensity data from (default = "counts").
run_col: Character string describing the Seurat meta.data column where the run identities are stored (default = NULL).
feature.metadata: Boolean value of whether the Seurat Object contains annotations stored in the feature metadata slot of the specified assay (default = FALSE).
verbose: Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = TRUE).

Value

A Cardinal object containing intensity values and feature metadata (annotations)

Examples

utils::str(formals(ConvertSeuratToCardinal))
#> Dotted pair list of 6
#>  $ data            : symbol 
#>  $ assay           : chr "Spatial"
#>  $ slot            : chr "counts"
#>  $ run_col         : NULL
#>  $ feature.metadata: logi FALSE
#>  $ verbose         : logi TRUE
# cardinal.obj <- ConvertSeuratToCardinal(SeuratObject, feature.metadata = TRUE)