annotateGiotto — annotateGiotto • Giotto

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)