Annotate giotto clustering#

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Last Updated: Mar 11, 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#

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

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