Reduce dimensions (PCA, TSNE, UMAP)

reduce_dims_scExp(
  scExp,
  dimension_reductions = c("PCA", "UMAP"),
  n = 50,
  batch_correction = FALSE,
  batch_list = NULL,
  remove_PC1 = FALSE,
  verbose = TRUE
)

Arguments

scExp	A SingleCellExperiment object.
dimension_reductions	A character vector of methods to apply. (c('PCA','TSNE','UMAP'))
n	Numbers of dimensions to keep for PCA. (50)
batch_correction	Do batch correction ? (FALSE)
batch_list	List of characters. Names are batch names, characters are sample names.
remove_PC1	Remove PC1 before UMAP & T-SNE, as probably correlated to library size ? Recommended when using 'TFIDF' normalization method. (FALSE)
verbose	Print messages ?(TRUE)

Value

A SingleCellExperiment object containing feature spaces. See ?reduceDims().

Examples


scExp = create_scExp(create_scDataset_raw()$mat,create_scDataset_raw()$annot)
#> ChromSCape::create_scExp - the matrix has 300 cells and 600 features.
scExp = reduce_dims_scExp(scExp,dimension_reductions=c("PCA","UMAP"))
#> Warning: ChromSCape::reduce_dims_scExp - The raw counts are not
#>                 normalized, running dimensionality reduction on raw counts.
scExp = normalize_scExp(scExp)
scExp = reduce_dims_scExp(scExp,dimension_reductions=c("PCA","UMAP"))