Set spatial locations#

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Last Updated: Mar 11, 2023

Description#

Function to set a spatial location slot

Usage#

set_spatial_locations(
  gobject,
  spatlocs,
  spat_unit = NULL,
  spat_loc_name = "raw",
  provenance = NULL,
  verbose = TRUE,
  set_defaults = TRUE
)

Arguments#

`gobject`	giotto object
`spatlocs`	spatial locations (accepts either `data.table` or `spatLocsObj`)
`spat_unit`	spatial unit (e.g. “cell”)
`spat_loc_name`	name of spatial locations, default “raw”
`provenance`	provenance information (optional)
`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.

Details#

If a spatLocsObj is provided to spatlocs param then any attached name and spat_unit info will be used for input to this function’s spat_loc_name and spat_unitparams, BUT will be overridden by any alternative specific inputs to those params.

ie: a spatLocsObj with spat_unit slot == ‘cell’ will be automatically nested by spat_unit ‘cell’ when using set_spatial_locations as long as param spat_unit = NULL. BUT if param spat_unit = 'nucleus' then the spatLocsObj will be nested by spat_unit ‘nucleus’ instead and its spat_unit slot will be changed to ‘nucleus’

Value#

giotto object

See Also#

Other spatial location data accessor functions: get_spatial_locations()

Other functions to set data in giotto object: get_cell_id(), get_feat_id(), set_NearestNetwork(), set_cell_id(), set_cell_metadata(), set_dimReduction(), set_expression_values(), set_feat_id(), set_feature_info(), set_feature_metadata(), set_giottoImage(), set_polygon_info(), set_spatialGrid(), set_spatialNetwork(), set_spatial_enrichment()