Set dimension reduction#

Last Updated: Nov 17, 2023

Description#

Function to set a dimension reduction slot

Usage#

set_dimReduction(
  gobject,
  dimObject,
  spat_unit = NULL,
  feat_type = NULL,
  reduction = c("cells", "genes"),
  reduction_method = c("pca", "umap", "tsne"),
  name = "pca",
  provenance = NULL,
  verbose = TRUE,
  set_defaults = TRUE
)

Arguments#

gobject

giotto object

dimObject

dimension object result to set

spat_unit

spatial unit (e.g. “cell”)

feat_type

feature type (e.g. “rna”, “dna”, “protein”)

reduction

reduction on cells or features

reduction_method

reduction method (e.g. “pca”)

name

name of reduction results

provenance

provenance information (optional)

verbose

be verbose

set_defaults

set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.

Value#

giotto object

See Also#

Other dimensional reduction data accessor functions: get_dimReduction()

Other functions to set data in giotto object: get_cell_id(), get_feat_id(), set_NearestNetwork(), set_cell_id(), set_cell_metadata(), set_expression_values(), set_feat_id(), set_feature_info(), set_feature_metadata(), set_giottoImage(), set_polygon_info(), set_spatialGrid(), set_spatialNetwork(), set_spatial_enrichment(), set_spatial_locations()