annotateGiotto: Annotate giotto clustering
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

annotateGiotto

R Documentation

Annotate giotto clustering

Converts cluster results into a user provided annotation.

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

`gobject`	giotto object
`spat_unit`	spatial unit
`feat_type`	feature type
`annotation_vector`	named annotation vector (names = cluster ids)
`cluster_column`	cluster column to convert to annotation names
`name`	new name for annotation column

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)