getSpatialLocations: Get spatial locations
| getSpatialLocations | R Documentation |
Get spatial locations
Description
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") |
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. |
spat_loc_name |
name of spatial locations (defaults to first name in spatial_locs slot, e.g. "raw") |
Value
data.table with coordinates or spatLocsObj depending on output
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()
