getDimReduction: Get dimension reduction

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Get dimension reduction

Description

Function to get a dimension reduction object

Usage

getDimReduction(
  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: get_dimReduction(), setDimReduction(), set_dimReduction()

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

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