Set nearest network#

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Last Updated: Mar 11, 2023

Description#

Set a NN-network for a Giotto object

Usage#

set_NearestNetwork(
  gobject,
  nn_network,
  spat_unit = NULL,
  feat_type = NULL,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  provenance = NULL,
  verbose = TRUE,
  set_defaults = TRUE
)

Arguments#

`gobject`	giotto object
`nn_network`	nnNetObj or igraph nearest network object. Data.table not yet supported.
`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
`provenance`	provenance information (optional)
`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.

Value#

giotto object

See Also#

Other expression space nearest network accessor functions: get_NearestNetwork()

Other functions to set data in giotto object: get_cell_id(), get_feat_id(), set_cell_id(), set_cell_metadata(), set_dimReduction(), set_expression_values(), set_feat_id(), set_feature_info(), set_feature_metadata(), set_giottoImage(), set_polygon_info(), set_spatialGrid(), set_spatialNetwork(), set_spatial_enrichment(), set_spatial_locations()