Converts cluster results into a user provided annotation.

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

Arguments

gobject

giotto object

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 specifify 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

data(mini_giotto_single_cell)

# show leiden clustering results
cell_metadata = pDataDT(mini_giotto_single_cell)
cell_metadata[['leiden_clus']]

# create vector with cell type names as names of the vector
clusters_cell_types = c('cell_type_1', 'cell_type_2', 'cell_type_3')
names(clusters_cell_types) = 1:3

# convert cluster results into annotations and add to cell metadata
mini_giotto_single_cell = annotateGiotto(gobject = mini_giotto_single_cell,
                                         annotation_vector = clusters_cell_types,
                                         cluster_column = 'leiden_clus', name = 'cell_types2')

# visualize annotation results
spatDimPlot(gobject = mini_giotto_single_cell,
            cell_color = 'cell_types2',
            spat_point_size = 3, dim_point_size = 3)