Get a NN-network from a Giotto object
Usage
get_NearestNetwork(
gobject,
spat_unit = NULL,
feat_type = NULL,
nn_network_to_use = NULL,
network_name = NULL,
output = c("nnNetObj", "igraph", "data.table"),
set_defaults = TRUE
)Arguments
- gobject
giotto object
- 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
- output
return a igraph or data.table object. Default 'igraph'
- set_defaults
set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.
See also
Other expression space nearest network accessor functions:
getNearestNetwork(),
setNearestNetwork(),
set_NearestNetwork()
Other functions to get data from giotto object:
getDimReduction(),
getExpression(),
getFeatureInfo(),
getGiottoImage(),
getMultiomics(),
getNearestNetwork(),
getPolygonInfo(),
getSpatialEnrichment(),
getSpatialGrid(),
getSpatialLocations(),
getSpatialNetwork(),
get_dimReduction(),
get_feature_info(),
get_giottoImage(),
get_multiomics(),
get_polygon_info(),
get_spatialGrid(),
get_spatialNetwork(),
get_spatial_enrichment(),
get_spatial_locations()