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Get dimension reduction

get_dimReduction.Rd

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", "matrix"),
  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 'matrix' 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: getDimReduction(), setDimReduction(), set_dimReduction()

Other functions to get data from giotto object: getDimReduction(), getExpression(), getFeatureInfo(), getGiottoImage(), getMultiomics(), getNearestNetwork(), getPolygonInfo(), getSpatialEnrichment(), getSpatialGrid(), getSpatialLocations(), getSpatialNetwork(), get_NearestNetwork(), get_feature_info(), get_giottoImage(), get_multiomics(), get_polygon_info(), get_spatialGrid(), get_spatialNetwork(), get_spatial_enrichment(), get_spatial_locations()