setDimReduction: Set dimension reduction data

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Set dimension reduction data

Description

Function to dimension reduction information into the Giotto object.

Usage

setDimReduction(
  gobject,
  x,
  spat_unit = NULL,
  feat_type = NULL,
  name = "pca",
  reduction = c("cells", "feats"),
  reduction_method = c("pca", "umap", "tsne"),
  provenance = NULL,
  verbose = TRUE,
  initialize = TRUE
)

Arguments

gobject	giotto object
x	dimObj or list of dimObj to set. Passing NULL will remove a specified set of dimension reduction information from the gobject
spat_unit	spatial unit (e.g. "cell")
feat_type	feature type (e.g. "rna", "dna", "protein")
name	name of reduction results
reduction	reduction on cells or features
reduction_method	reduction method (e.g. "pca")
provenance	provenance information (optional)
verbose	be verbose
initialize	(default = FALSE) whether to initialize the gobject before returning

Value

giotto object

See Also

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

Other functions to set data in giotto object: get_cell_id(), get_feat_id(), setCellMetadata(), setExpression(), setFeatureInfo(), setFeatureMetadata(), setGiottoImage(), setMultiomics(), setNearestNetwork(), setPolygonInfo(), setSpatialEnrichment(), setSpatialGrid(), setSpatialLocations(), setSpatialNetwork(), set_NearestNetwork(), set_cell_id(), set_cell_metadata(), set_dimReduction(), 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.