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Extract spatial coordinates and cluster information

Source: R/GetBoundary.R
ExtractCoords.Rd

Extract spatial coordinates and (optionally) cluster assignments from a Seurat object, a SpatialExperiment object, or a user-supplied data frame.

Usage

extractCoords(data, cluster_col = NULL, extract_cluster = TRUE, ...)

Arguments

data

A Seurat object, a SpatialExperiment object, or a data frame containing spatial coordinates.

cluster_col

Character scalar specifying the metadata column name containing cluster assignments. If NULL, a default is used depending on the input object type:

  • "seurat_clusters" for Seurat objects

  • "cluster" for SpatialExperiment objects

extract_cluster

Logical indicating whether to extract cluster information. If FALSE, only spatial coordinates and cell IDs are returned. Default is TRUE.

...

Additional arguments (unused).

Value

A data frame with columns x, y, and cell, and optionally cluster.

Details

This is an S3 generic with methods implemented for Seurat, SpatialExperiment, and data.frame.

Examples

coords <- readRDS(system.file(
    "extdata", "MouseBrainCoords.rds",
    package = "SpNeigh"
))

head(extractCoords(coords))
#>   cell        x        y cluster
#> 1    1 1898.815 2540.963       4
#> 2    2 1895.305 2532.627       4
#> 3    3 2368.073 2534.409       2
#> 4    4 1903.726 2560.010       4
#> 5    5 1917.481 2543.132       4
#> 6    6 1926.540 2560.044       4

head(extractCoords(coords, extract_cluster = FALSE))
#>   cell        x        y
#> 1    1 1898.815 2540.963
#> 2    2 1895.305 2532.627
#> 3    3 2368.073 2534.409
#> 4    4 1903.726 2560.010
#> 5    5 1917.481 2543.132
#> 6    6 1926.540 2560.044