Get nearest network#

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Last Updated: Mar 11, 2023

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: set_NearestNetwork()

Other functions to get data from giotto object: get_dimReduction(), get_expression_values(), get_feature_info(), get_giottoImage(), get_polygon_info(), get_spatialGrid(), get_spatialNetwork(), get_spatial_enrichment(), get_spatial_locations()