Get feature metadata from giotto object
Usage
getFeatureMetadata(
gobject,
spat_unit = NULL,
feat_type = NULL,
output = c("featMetaObj", "data.table"),
copy_obj = TRUE,
set_defaults = TRUE
)Arguments
- gobject
giotto object
- spat_unit
spatial unit (e.g. "cell")
- feat_type
feature type (e.g. "rna", "dna", "protein")
- output
return as either 'data.table' or 'featMetaObj'
- copy_obj
whether to perform a deepcopy of the data.table information
- 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
fDataDT
Other functions to get data from giotto object:
getCellMetadata(),
getDimReduction(),
getExpression(),
getFeatureInfo(),
getGiottoImage(),
getMultiomics(),
getNearestNetwork(),
getPolygonInfo(),
getSpatialEnrichment(),
getSpatialGrid(),
getSpatialLocations(),
getSpatialNetwork(),
get_multiomics()
Examples
g <- GiottoData::loadGiottoMini("vizgen")
#> 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"
getFeatureMetadata(g)
#> An object of class featMetaObj
#> spat_unit : "z0"
#> feat_type : "rna"
#> provenance: z0
#>
#> feat_ID
#> <char>
#> 1: Mlc1
#> 2: Gprc5b
#> 3: Gfap