Function to get a dimension reduction object
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.
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()
Examples
g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#> active environment : 'giotto_env'
#> python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/share/miniconda/envs/giotto_env/bin/python"
getDimReduction(g)
#> An object of class dimObj : "pca"
#> --| Contains dimension reduction generated with: pca
#> ----| for feat_type: rna
#> ----| spat_unit: cell
#>
#> 100 dimensions for 624 data points
#>
#> Additional included info:
#> [1] "eigenvalues" "loadings"
#>