getSpatialLocations: Get spatial locations

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

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()

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.