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
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_feature_metadata(),
set_giottoImage(),
set_multiomics(),
set_polygon_info(),
set_spatialGrid(),
set_spatialNetwork(),
set_spatial_enrichment(),
set_spatial_locations()