Get dimension reduction#

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Last Updated: Mar 11, 2023

Description#

Function to get a dimension reduction object

Usage#

get_dimReduction(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  reduction = c("cells", "feats"),
  reduction_method = c("pca", "umap", "tsne"),
  name = "pca",
  output = c("dimObj", "data.table"),
  set_defaults = TRUE
)

Arguments#

`gobject`	giotto object
`spat_unit`	spatial unit (e.g. “cell”)
`feat_type`	feature type (e.g. “rna”, “dna”, “protein”)
`reduction`	reduction on cells or features (e.g. “cells”, “feats”)
`reduction_method`	reduction method (e.g. “pca”, “umap”, “tsne”)
`name`	name of reduction results
`output`	object type to return as. Either ‘dimObj’ (default) or ‘data.table of the embedding coordinates.
`set_defaults`	set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.

Value#

dim reduction object (default) or dim reduction coordinates

See Also#

Other dimensional reduction data accessor functions: set_dimReduction()

Other functions to get data from giotto object: get_NearestNetwork(), get_expression_values(), get_feature_info(), get_giottoImage(), get_polygon_info(), get_spatialGrid(), get_spatialNetwork(), get_spatial_enrichment(), get_spatial_locations()