R/umap.R

In flowSpy: A Toolkit for Flow And Mass Cytometry Data

#'
#' Calculating UMAP
#'
#' @name runUMAP
#'
#' @description
#' Calculate Uniform Manifold Approximation and Projection in FSPY
#'
#' @param object an FSPY object
#' @param umap.config object of class umap.config. See \code{\link[umap]{umap}}.
#' @param n_neighbors numeric. Number of neighbors
#' @param dims numeric. Dim of umap, you can also change it in umap.config.
#' @param verbose logical. Whether to print calculation progress.
#' @param ... Options to pass on to the \code{\link[umap]{umap}} function
#'
#' @import umap
#' @seealso \code{\link[umap]{umap}}
#' @return An FSPY object
#'
#' @export
#'
#' @examples
#'
#' if (FALSE) {
#'
#' fspy <- runUMAP(fspy, verbose = TRUE)
#' fspy <- runUMAP(fspy, n_neighbors = 20, verbose = TRUE)
#'
#' }
#'
#'
runUMAP <- function(object, umap.config = umap.defaults,
                    n_neighbors = 30, dims = 2, verbose = FALSE, ...) {
  if (verbose) message(Sys.time(), " [INFO] Calculating Umap.")
  if (length(which(object@meta.data$dowsample == 1)) < 10) stop(Sys.time, " [ERROR] Not enough cells, please run processingCluster and choose correct downsampling.size paramter. ")
  mat <- as.matrix(object@log.data[which(object@meta.data$dowsample == 1), ])

  umap.config$n_neighbors <- n_neighbors
  umap.config$n_components <- dims
  umap.out <- umap(mat, config = umap.config, ...)
  object@umap.value <- umap.out$layout
  colnames(object@umap.value) <- paste0("UMAP_", 1:ncol(umap.out$layout))
  rownames(object@umap.value) <- rownames(mat)

  if (verbose) message(Sys.time(), " [INFO] Calculating Umap.")
  return(object)
}