set_NearestNetwork: Set nearest network

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Set nearest network

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,
  initialize = FALSE
)

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.
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(), setNearestNetwork()

Other functions to set data in giotto object: get_cell_id(), get_feat_id(), setCellMetadata(), setDimReduction(), setExpression(), setFeatureInfo(), setFeatureMetadata(), setGiottoImage(), setMultiomics(), setNearestNetwork(), setPolygonInfo(), setSpatialEnrichment(), setSpatialGrid(), setSpatialLocations(), setSpatialNetwork(), 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.