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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

  • "cluster" for data.frame 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 containing columns x, y, and cell, and optionally cluster. For Seurat and SpatialExperiment inputs, only these standardized columns are returned. For data.frame input, additional columns present in the input may also be retained.

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

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