reduce_dims_sce: Calculate dimensionality reductions for a...

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Calculate dimensionality reductions for a SingleCellExperiment object or merged SingleCellExperiment objects using tSNE, UMAP, UMAP3D

Description

Calculate dimensionality reductions for a SingleCellExperiment object or merged SingleCellExperiment objects using tSNE, UMAP, UMAP3D

Usage

reduce_dims_sce(
  sce,
  input_reduced_dim = c("PCA", "Liger"),
  reduction_methods = c("tSNE", "UMAP", "UMAP3D"),
  vars_to_regress_out = NULL,
  pca_dims = 20,
  ...
)

Arguments

sce	a SingleCellExperiment object or merged sce objects
input_reduced_dim	the input reducedDim
reduction_methods	one or more of "tSNE","UMAP","UMAP3D"
vars_to_regress_out	Variables to regress out before dimensionality reduction.
pca_dims	the number of pca dimensions used
...	see uwot::umap for umap options

Value

sce SingleCellExperiment object annotated with reducedDims

See Also

Other clustering and dimensionality reduction: .get_x_most_specific_genes(), .map_celltypes(), .map_celltypes_with_ewce(), cluster_sce(), map_custom_celltypes()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.