Annotate giotto clustering#
Last Updated: Sep 07, 2023
Description#
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#
|
giotto object |
|
spatial unit |
|
feature type |
|
named annotation vector (names = cluster ids) |
|
cluster column to convert to annotation names |
|
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:
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