set_cell_id: Set cell IDs for a given spatial unit

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Set cell IDs for a given spatial unit

Description

Setter function for the cell_ID slot. Directly replaces (sets) this slot

Usage

set_cell_id(
  gobject,
  spat_unit = NULL,
  cell_IDs,
  set_defaults = TRUE,
  verbose = TRUE
)

Arguments

gobject	giotto object
spat_unit	spatial unit (e.g. "cell")
cell_IDs	character vector of cell IDs to set. (See details)
set_defaults	set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.
verbose	be verbose

Details

Data for each spatial unit is expected to agree on a single set of cell_IDs that are shared across any feature types. These cell_IDs are stored within the giotto object's cell_ID slot.

Pass NULL to cell_IDs param in order to delete the entry.
Pass 'initialize' to cell_IDs param in order to initialize the specified entry.

NOTE: The main purpose of the setter is to initialize, as cell_ID values are AUTOMATICALLY updated every time initialize() is called on the giotto object.

Value

giotto object with set cell_ID slot

See Also

get_cell_id

Other functions to set data in giotto object: get_cell_id(), get_feat_id(), setCellMetadata(), setDimReduction(), setExpression(), setFeatureInfo(), setFeatureMetadata(), setGiottoImage(), setMultiomics(), setNearestNetwork(), setPolygonInfo(), setSpatialEnrichment(), setSpatialGrid(), setSpatialLocations(), setSpatialNetwork(), set_NearestNetwork(), set_cell_metadata(), set_dimReduction(), set_expression_values(), set_feat_id(), set_feature_info(), set_giottoImage(), set_multiomics(), set_polygon_info(), set_spatialGrid(), set_spatialNetwork(), set_spatial_enrichment(), set_spatial_locations()

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.