getSpatialNetwork: Get spatial network

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Get spatial network

Description

Function to get a spatial network

Usage

getSpatialNetwork(
  gobject,
  spat_unit = NULL,
  name = NULL,
  output = c("spatialNetworkObj", "networkDT", "networkDT_before_filter", "outputObj"),
  set_defaults = TRUE,
  copy_obj = TRUE,
  verbose = TRUE
)

Arguments

gobject	giotto object
spat_unit	spatial unit (e.g. "cell")
name	name of spatial network
output	object type to return as. Options: 'spatialNetworkObj' (default), 'networkDT' and 'networkDT_before_filter' for data.table outputs.
set_defaults	set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.
copy_obj	whether to copy/duplicate when getting the object (default = TRUE)
verbose	be verbose

See Also

Other spatial network data accessor functions: get_spatialNetwork(), setSpatialNetwork(), set_spatialNetwork()

Other functions to get data from giotto object: getDimReduction(), getExpression(), getFeatureInfo(), getGiottoImage(), getMultiomics(), getNearestNetwork(), getPolygonInfo(), getSpatialEnrichment(), getSpatialGrid(), getSpatialLocations(), 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.