Get cell metadata from giotto object
Usage
getCellMetadata(
gobject,
spat_unit = NULL,
feat_type = NULL,
output = c("cellMetaObj", "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 'cellMetaObj'
- copy_obj
whether to deep copy/duplicate when getting the object (default = TRUE)
- 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
pDataDT
Other functions to get data from giotto object:
getDimReduction(),
getExpression(),
getFeatureInfo(),
getFeatureMetadata(),
getGiottoImage(),
getMultiomics(),
getNearestNetwork(),
getPolygonInfo(),
getSpatialEnrichment(),
getSpatialGrid(),
getSpatialLocations(),
getSpatialNetwork(),
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"
getCellMetadata(g)
#> An object of class cellMetaObj
#> spat_unit : "cell"
#> feat_type : "rna"
#> provenance: cell
#> dimensions: 624 7
#>
#> cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus
#> <char> <int> <int> <num> <num> <num>
#> 1: AACTCGATGGCGCAGT-1 1 265 41.79811 1057.9308 2
#> 2: GGCTGGCTAGCTTAAA-1 1 279 44.00631 1064.7493 5
#> 3: GACGCCTGTTGCAGGG-1 1 219 34.54259 964.9294 2
#> custom_leiden
#> <num>
#> 1: 4
#> 2: 3
#> 3: 3