R/get_faust_markers_and_levels.R

In MiguelRodo/faustutils: Additional functions to extract and plot FAUST output

#' @title Get the number of levels used for each marker FAUST used to cluster
#'
#' @description
#' Gives the markers FAUST used and the number of levels used per such marker.
#' Note that it only works after the SCAMP clustering has been performed, i.e.
#' not simply after the annotations have been approved.
#'
#' @inheritParams save_faust_pop
#'
#' @return \code{Character vector}
#' @export
get_faust_markers_and_levels <- function(project_path){

  #
  cluster_name <- readRDS(file.path(project_path, 'faustData', 'metaData', 'scampClusterNames.rds'))[1]

  # all channels considered
  active_chnl_vec <- readRDS(file.path(project_path, 'faustData', 'metaData', 'activeChannels.rds'))

  # filter all channels considered to get all channels used
  clustered_chnl_vec <- NULL
  for(x in active_chnl_vec) if(stringr::str_detect(cluster_name, x)) clustered_chnl_vec <- c(clustered_chnl_vec, x)

  # get observed levels for each channel used
  n_level_vec <- setNames(rep(NA, length(clustered_chnl_vec)), clustered_chnl_vec)
  for(i in seq_along(clustered_chnl_vec)){
    n_level_loc <- stringr::str_locate(cluster_name, clustered_chnl_vec[i])[,"end"][[1]] + 4

    n_level_vec[i] <- as.numeric(stringr::str_sub(cluster_name, n_level_loc, n_level_loc))
  }
  n_level_vec
}