get_NearestNetwork: Get nearest network

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Get nearest network

Description

Get a NN-network from a Giotto object

Usage

get_NearestNetwork(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  nn_network_to_use = NULL,
  network_name = NULL,
  output = c("nnNetObj", "igraph", "data.table"),
  set_defaults = TRUE
)

Arguments

gobject	giotto object
spat_unit	spatial unit (e.g. "cell")
feat_type	feature type (e.g. "rna", "dna", "protein")
nn_network_to_use	"kNN" or "sNN"
network_name	name of NN network to be used
output	return a igraph or data.table object. Default 'igraph'
set_defaults	set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.

Value

igraph or data.table object

See Also

Other expression space nearest network accessor functions: getNearestNetwork(), setNearestNetwork(), set_NearestNetwork()

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