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

Source: R/reduce_dims_sce.R

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

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()