Annotate Giotto object — annotateGiotto • GiottoClass

Map user provided annotations/labels based on another existing metadata column (usually clustering labels)

Usage

annotateGiotto(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  annotation_vector = NULL,
  cluster_column = NULL,
  name = "cell_types"
)

Arguments

gobject: giotto object
spat_unit: spatial unit
feat_type: feature type
annotation_vector: named character vector. Vector names are labels in the cluster column. Labels to assign are the vector values.
cluster_column: character. Cell metaadata column to map annotation values based on.
name: new name for annotation column

Value

giotto object

Details

You need to specify which (cluster) column you want to annotate and you need to provide an annotation vector like this:

1. identify the cell type of each cluster
2. create a vector of these cell types, e.g. cell_types = c('T-cell', 'B-cell', 'Stromal')
3. provide original cluster names to previous vector, e.g. names(cell_types) = c(2, 1, 3)

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"
)