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Get spatial locations
getSpatialLocations.Rd
Function to get a spatial location data.table
Usage
getSpatialLocations(
gobject,
spat_unit = NULL,
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")
- 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.
See also
Other spatial location data accessor functions:
get_spatial_locations()
,
setSpatialLocations()
,
set_spatial_locations()
Other functions to get data from giotto object:
getDimReduction()
,
getExpression()
,
getFeatureInfo()
,
getGiottoImage()
,
getMultiomics()
,
getNearestNetwork()
,
getPolygonInfo()
,
getSpatialEnrichment()
,
getSpatialGrid()
,
getSpatialNetwork()
,
get_NearestNetwork()
,
get_dimReduction()
,
get_feature_info()
,
get_giottoImage()
,
get_multiomics()
,
get_polygon_info()
,
get_spatialGrid()
,
get_spatialNetwork()
,
get_spatial_enrichment()
,
get_spatial_locations()