Get dimension reduction#
Last Updated: Oct 02, 2023
Description#
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", "data.table"),
set_defaults = TRUE
)
Arguments#
|
giotto object |
|
spatial unit (e.g. “cell”) |
|
feature type (e.g. “rna”, “dna”, “protein”) |
|
reduction on cells or features (e.g. “cells”, “feats”) |
|
reduction method (e.g. “pca”, “umap”, “tsne”) |
|
name of reduction results |
|
object type to return as. Either ‘dimObj’ (default) or ‘data.table of the embedding coordinates. |
|
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:
set_dimReduction()
Other functions to get data from giotto object:
get_NearestNetwork()
, get_expression_values()
,
get_feature_info()
, get_giottoImage()
, get_polygon_info()
,
get_spatialGrid()
, get_spatialNetwork()
,
get_spatial_enrichment()
, get_spatial_locations()