Get nearest neighbor network

Get a NN-network from a Giotto object

Usage

getNearestNetwork(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  nn_type = NULL,
  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_type

"kNN" or "sNN"

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: get_NearestNetwork(), setNearestNetwork(), set_NearestNetwork()

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