annotateGiotto: annotateGiotto

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

annotateGiotto

Description

Converts cluster results into a user provided annotation.

Usage

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

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)

Value

giotto object

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)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.