reduce_dims_scExp {ChromSCape} | R Documentation |
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 )
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) |
A SingleCellExperiment object containing feature spaces. See ?reduceDims().
raw <- create_scDataset_raw() scExp = create_scExp(raw$mat, raw$annot) scExp = reduce_dims_scExp(scExp,dimension_reductions=c("PCA","UMAP")) scExp = normalize_scExp(scExp) scExp = reduce_dims_scExp(scExp,dimension_reductions=c("PCA","UMAP"))