Merge tiled cellspec objects using centroid ownership

Every centroid is assigned to the half open outer box containing it. A centroid found in more than one box is an error. Cells in a tile whose centroid is owned by another tile, or by no tile, are treated as halo cells and dropped.

Usage

cs_merge_tiles(tiles, tile_bounds, ownership = "centroid", tolerance = 1e-09)

Arguments

tiles

A named or positional list of cellspec tile objects. Names, when supplied, must equal tile_bounds$tile_id.

tile_bounds

A data frame with tile_id, xmin, xmax, ymin and ymax in micrometres.

ownership

Ownership method. The only supported value is "centroid".

tolerance

Non-negative tolerance used to snap coordinates close to a box boundary before applying its half open comparisons.

Value

A merged cellspec object.

See also

Other object: cs_accessors, cs_bind(), cs_example(), cs_features(), cs_new(), is_cellspec()

Examples

tile_bounds <- data.frame(
  tile_id = "tile-1", xmin = 0, xmax = 10000, ymin = 0, ymax = 10000
)
cs_merge_tiles(list(cs_example()), tile_bounds)
#> <cellspec> spec 1.0.0
#>   cells     80 in 2 images (2 samples)
#>   features  19: 16 intensity, 2 shape, 1 other
#>   markers   4: DAPI, CD3e, Pan-Cytokeratin, FOXP3
#>   pixel     0.5 um/px
#>   adjacency none
#>   source    cs_merge_tiles 1.0.0 (cellspecR simulator 1.1.0)