R/umap.R

In whtns/varbintools: Sequence Based Copy Number Detection Using Variable Bin Lengths

#' make umap of varbin data
#'
#' @param df
#'
#' @return
#' @export
#'
#' @examples
varbin_umap <- function(seg_df_cells_t) {
  # subsetting only the cells

  set.seed(42)
  dat_umap <- uwot::umap(seg_df_cells_t,
                         metric = "manhattan",
                         min_dist = 0,
                         n_neighbors = 40)

  umap_df <- as.data.frame(dat_umap) %>%
    dplyr::rename("umap1" = "V1",
                  "umap2" = "V2")

  rownames(umap_df) <- rownames(seg_df_cells_t)

  # We can visualize the result of the dimension reduction.

  umap_df %>%
    rownames_to_column(var = "Cell") %>%
    identity()

  return(umap_df)
}