Function to get a spatial network
Usage
getSpatialNetwork(
gobject,
spat_unit = NULL,
name = NULL,
output = c("spatialNetworkObj", "networkDT", "networkDT_before_filter", "outputObj"),
set_defaults = TRUE,
copy_obj = TRUE,
verbose = TRUE,
simplify = TRUE
)Arguments
- gobject
giotto object
- spat_unit
spatial unit (e.g. "cell")
- name
name of spatial network
- output
object type to return as. Options: 'spatialNetworkObj' (default), 'networkDT' and 'networkDT_before_filter' for data.table outputs.
- set_defaults
set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.
- copy_obj
whether to copy/duplicate when getting the object (default = TRUE)
- verbose
be verbose
- simplify
logical. Whether or not to take object out of a list when there is a length of 1.
See also
Other spatial network data accessor functions:
setSpatialNetwork()
Other functions to get data from giotto object:
getCellMetadata(),
getDimReduction(),
getExpression(),
getFeatureInfo(),
getFeatureMetadata(),
getGiottoImage(),
getMultiomics(),
getNearestNetwork(),
getPolygonInfo(),
getSpatialEnrichment(),
getSpatialGrid(),
getSpatialLocations(),
get_multiomics()
Examples
g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#> active environment : 'giotto_env'
#> python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/share/miniconda/envs/giotto_env/bin/python"
getSpatialNetwork(g)
#> An object of class spatialNetworkObj : "Delaunay_network"
#> Contains spatial network generated with: deldir
#> spat_unit : "cell"
#> provenance: cell
#> 1770 connections (filtered)
#> 1814 connections (before filter)
#>