Get spatial locations#

Last Updated: Sep 07, 2023

Description#

Function to get a spatial location data.table

Usage#

get_spatial_locations(
  gobject,
  spat_unit = NULL,
  spat_loc_name = NULL,
  output = c("spatLocsObj", "data.table"),
  copy_obj = TRUE,
  verbose = TRUE,
  set_defaults = TRUE
)

Arguments#

`gobject`	giotto object
`spat_unit`	spatial unit (e.g. “cell”)
`spat_loc_name`	name of spatial locations (defaults to first name in spatial_locs slot, e.g. “raw”)
`output`	what object type to get the spatial locations as. Default is as a ‘spatLocsObj’. Returning as ‘data.table’ is also possible.
`copy_obj`	whether to copy/duplicate when getting the object (default = TRUE)
`verbose`	be verbose
`set_defaults`	set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.

Value#

data.table with coordinates or spatLocsObj depending on output

See Also#

Other spatial location data accessor functions: set_spatial_locations()

Other functions to get data from giotto object: get_NearestNetwork(), get_dimReduction(), get_expression_values(), get_feature_info(), get_giottoImage(), get_polygon_info(), get_spatialGrid(), get_spatialNetwork(), get_spatial_enrichment()