Annotate giotto clustering

Converts cluster results into a user provided annotation.

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 annotation vector (names = cluster ids)

cluster_column

cluster column to convert to annotation names

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"
)