R/reduce_dimensions.R

In CBMR-Single-Cell-Omics-Platform/SCOPfunctions: Single Cell Omics Platform Functions

#' Estimate dataset dimensionality
#'
#' @param x : Seurat or SingleCellExperiment object
#' @param max_dim : max number of dimensions to try
#' @param seed.use : random seed
#'
#' @return integer number of dimensions, <= max_dim
#' @export
#'
#' @examples estimate_dimensions(seurat_obj)
dim_red_est <- function(x,
                        max_dim=75,
                        seed.use=12345) {

  if(is(x, "SingleCellExperiment")) {
    x <- as.Seurat(x)
  }

  x %>% RunPCA(., npcs=max_dim, seed.use=seed.use, verbose = F) -> x

  dims <- round(as.numeric(intrinsicDimension::maxLikGlobalDimEst(data = x@reductions$pca[, 1:max_dim], k = 20)))

  return(dims)
}