Set nearest neighbor network

Set a NN-network for a Giotto object

Usage

setNearestNetwork(
  gobject,
  x,
  spat_unit = NULL,
  feat_type = NULL,
  nn_type = "sNN",
  name = "sNN.pca",
  provenance = NULL,
  verbose = TRUE,
  initialize = TRUE
)

Arguments

gobject

giotto object

x

nnNetObj or list of nnNetObj. Passing NULL will remove a specified set of nearest neighbor network information from the gobject

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 yet supported.

provenance

provenance information (optional)

verbose

be verbose

initialize

(default = FALSE) whether to initialize the gobject before returning

Value

giotto object

See also

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

Other functions to set data in giotto object: get_cell_id(), get_feat_id(), setCellMetadata(), setDimReduction(), setExpression(), setFeatureInfo(), setFeatureMetadata(), setGiottoImage(), setMultiomics(), setPolygonInfo(), setSpatialEnrichment(), setSpatialGrid(), setSpatialLocations(), setSpatialNetwork(), set_NearestNetwork(), set_cell_id(), set_cell_metadata(), set_dimReduction(), set_expression_values(), set_feat_id(), set_feature_info(), set_feature_metadata(), set_giottoImage(), set_multiomics(), set_polygon_info(), set_spatialGrid(), set_spatialNetwork(), set_spatial_enrichment(), set_spatial_locations()