Convert Cluster Results Into User Provided Annotation

annotateGiotto()

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

A 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

data(mini_giotto_single_cell)

# show leiden clustering results
cell_metadata = pDataDT(mini_giotto_single_cell)
cell_metadata[['leiden_clus']]
#>  [1] 3 3 1 3 2 3 2 2 2 1 1 3 1 1 1 1 1 1 2 2
# 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)

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