Method to extract coordinates

Usage

GetCoordinates(object)

# S4 method for class 'Staffli'
GetCoordinates(object)

# S4 method for class 'Seurat'
GetCoordinates(object)

Arguments

object: A Staffli or Seurat object

Value

A tbl with spot coordinates

Examples


# Load example data
se_mbrain <- readRDS(system.file("extdata/mousebrain", "se_mbrain", package = "semla")) |> 
   LoadImages()
#> 
#> ── Loading H&E images ──
#> 
#> ℹ Loading image from /private/var/folders/8r/bfm2m_q17znfk0m_8dt330tm0000gp/T/RtmpLHpYU7/temp_libpath305b1609463d/semla/extdata/mousebrain/spatial/tissue_lowres_image.jpg
#> ℹ Scaled image from 600x565 to 400x377 pixels
#> ℹ Saving loaded H&E images as 'rasters' in Seurat object

# Fetch Staffli object
staffli_object <- GetStaffli(se_mbrain)

# Fetch coordinates from a Staffli object
coordinates <- GetCoordinates(staffli_object)
coordinates
#> # A tibble: 2,560 × 6
#>    barcode                x     y pxl_col_in_fullres pxl_row_in_fullres sampleID
#>    <chr>              <int> <int>              <int>              <int>    <int>
#>  1 AAACAAGTATCTCCCA-1   102    50              12934              10718        1
#>  2 AAACACCAATAACTGC-1    19    59               4435              12308        1
#>  3 AAACATTTCCCGGATT-1    97    61              12420              12677        1
#>  4 AAACCCGAACGAAATC-1   115    45              14267               9830        1
#>  5 AAACCGGGTAGGTACC-1    28    42               5361               9282        1
#>  6 AAACCGTTCGTCCAGG-1    42    52               6792              11065        1
#>  7 AAACCTAAGCAGCCGG-1    83    65              10985              13387        1
#>  8 AAACGAGACGGTTGAT-1    79    35              10584               8043        1
#>  9 AAACGGGCGTACGGGT-1    91    65              11804              13388        1
#> 10 AAACGGTTGCGAACTG-1    59    67               8528              13739        1
#> # ℹ 2,550 more rows


# Fetch images from a Seurat object
coordinates <- GetCoordinates(se_mbrain)
coordinates
#> # A tibble: 2,560 × 6
#>    barcode                x     y pxl_col_in_fullres pxl_row_in_fullres sampleID
#>    <chr>              <int> <int>              <int>              <int>    <int>
#>  1 AAACAAGTATCTCCCA-1   102    50              12934              10718        1
#>  2 AAACACCAATAACTGC-1    19    59               4435              12308        1
#>  3 AAACATTTCCCGGATT-1    97    61              12420              12677        1
#>  4 AAACCCGAACGAAATC-1   115    45              14267               9830        1
#>  5 AAACCGGGTAGGTACC-1    28    42               5361               9282        1
#>  6 AAACCGTTCGTCCAGG-1    42    52               6792              11065        1
#>  7 AAACCTAAGCAGCCGG-1    83    65              10985              13387        1
#>  8 AAACGAGACGGTTGAT-1    79    35              10584               8043        1
#>  9 AAACGGGCGTACGGGT-1    91    65              11804              13388        1
#> 10 AAACGGTTGCGAACTG-1    59    67               8528              13739        1
#> # ℹ 2,550 more rows