FS map

Get and set fs_map tibble for a CellGraphAssay, CellGraphAssay5 or a Seurat object

Usage

FSMap(object, ...)

FSMap(object, ...) <- value

# S3 method for MPXAssay
FSMap(object, ...)

# S3 method for MPXAssay
FSMap(object, ...) <- value

# S3 method for Seurat
FSMap(object, ...)

# S3 method for Seurat
FSMap(object, ...) <- value

Arguments

object

An object containing arrow data

...

Not implemented

value

A tbl_df

Value

FSMap: An fs_map tibble

FSMap<-: An object with an updated fs_map tibble

See also

CellGraphs() for getting/setting CellGraph lists and PolarizationScores(),ColocalizationScores() for getting/setting spatial metrics

Examples

pxl_file <- system.file("extdata/five_cells",
                        "five_cells.pxl",
                        package = "pixelatorR")
seur_obj <- ReadMPX_Seurat(pxl_file)
#> ✔ Created a 'Seurat' object with 5 cells and 80 targeted surface proteins

# Check PXL file paths in a Seurat object
FSMap(seur_obj)
#> # A tibble: 1 × 3
#>   id_map           sample pxl_file                                              
#>   <list>            <int> <chr>                                                 
#> 1 <tibble [5 × 2]>      1 /private/var/folders/gw/bdcqhnvs0m9gs_mq8n51jtbc0000g…

if (FALSE) {
# Update PXL file paths in a Seurat object
new_pxl_file_paths <- c("<path_to_pxl_file>")
FSMap(seur_obj) <- FSMap(seur_obj) %>%
  mutate(pxl_file = new_pxl_file_paths)
}