Remove cell annotation

Removes cell annotation from a Giotto object for a specific feature modality (default = 'rna')

Usage

removeCellAnnotation(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  columns = NULL,
  return_gobject = TRUE
)

Arguments

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

columns

names of columns to remove

return_gobject

boolean: return giotto object (default = TRUE)

Value

giotto object

Details

if return_gobject = FALSE, it will return the cell metadata

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"

annotation <- c(
    "1" = "cell_type_1",
    "2" = "cell_type_2",
    "3" = "cell_type_3",
    "4" = "cell_type_4",
    "5" = "cell_type_5",
    "6" = "cell_type_6",
    "7" = "cell_type_7",
    "8" = "cell_type_8"
)

g <- annotateGiotto(g,
    annotation_vector = annotation,
    cluster_column = "leiden_clus"
)

g <- removeCellAnnotation(g, columns = "cell_types")