set_dimReduction: Set dimension reduction

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Set dimension reduction

Description

Function to set a dimension reduction slot

Usage

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

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.
initialize	(default = FALSE) whether to initialize the gobject before returning

Value

giotto object

See Also

Other dimensional reduction data accessor functions: getDimReduction(), get_dimReduction(), setDimReduction()

Other functions to set data in giotto object: get_cell_id(), get_feat_id(), setCellMetadata(), setDimReduction(), setExpression(), setFeatureInfo(), setFeatureMetadata(), setGiottoImage(), setMultiomics(), setNearestNetwork(), setPolygonInfo(), setSpatialEnrichment(), setSpatialGrid(), setSpatialLocations(), setSpatialNetwork(), set_NearestNetwork(), set_cell_id(), set_cell_metadata(), set_expression_values(), set_feat_id(), set_feature_info(), set_giottoImage(), set_multiomics(), set_polygon_info(), set_spatialGrid(), set_spatialNetwork(), set_spatial_enrichment(), set_spatial_locations()

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