setNearestNetwork: Set nearest neighbor network

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Set nearest neighbor network

Description

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_giottoImage(), set_multiomics(), set_polygon_info(), set_spatialGrid(), set_spatialNetwork(), set_spatial_enrichment(), set_spatial_locations()

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.