spatCellCellcom does not allow verbose='none' if do_parallel=TRUE

[rbutleriii]

I noticed in my output that spatCellCellcom still delivers the "simulation #" output even if you set verbose='none'. Looking at the function, it seems a quick fix:

  ## parallel option ##
  if(do_parallel == TRUE) {

    savelist = lapply_flex(X = 1:nrow(combn_DT), future.seed=TRUE, cores = cores, fun = function(row) {

      cell_type_1 = combn_DT[row][['V1']]
      cell_type_2 = combn_DT[row][['V2']]

      specific_scores = specificCellCellcommunicationScores(gobject = gobject,
                                                            feat_type = feat_type,
                                                            spat_unit = spat_unit,
                                                            cluster_column = cluster_column,
                                                            random_iter = random_iter,
                                                            cell_type_1 = cell_type_1,
                                                            cell_type_2 = cell_type_2,
                                                            feat_set_1 = feat_set_1,
                                                            feat_set_2 = feat_set_2,
                                                            spatial_network_name = spatial_network_name,
                                                            log2FC_addendum = log2FC_addendum,
                                                            min_observations = min_observations,
                                                            detailed = detailed,
                                                            adjust_method = adjust_method,
                                                            adjust_target = adjust_target,
                                                            set_seed = set_seed,
                                                            seed_number = seed_number) # no verbose passed

    })


  } else {

    ## for loop over all combinations ##
    savelist = list()
    countdown = nrow(combn_DT)

    for(row in 1:nrow(combn_DT)) {

      cell_type_1 = combn_DT[row][['V1']]
      cell_type_2 = combn_DT[row][['V2']]

      # <----------------------------------------------------- this all only exists in else
      if(verbose == 'a little' | verbose == 'a lot') cat('\n\n PROCESS nr ', countdown,': ', cell_type_1, ' and ', cell_type_2, '\n\n')

      if(verbose %in% c('a little', 'none')) { 
        specific_verbose = F
      } else {
        specific_verbose = T
      }
      # <----------------------------------------------------

      specific_scores = specificCellCellcommunicationScores(gobject = gobject,
                                                            feat_type = feat_type,
                                                            spat_unit = spat_unit,
                                                            cluster_column = cluster_column,
                                                            random_iter = random_iter,
                                                            cell_type_1 = cell_type_1,
                                                            cell_type_2 = cell_type_2,
                                                            feat_set_1 = feat_set_1,
                                                            feat_set_2 = feat_set_2,
                                                            spatial_network_name = spatial_network_name,
                                                            log2FC_addendum = log2FC_addendum,
                                                            min_observations = min_observations,
                                                            detailed = detailed,
                                                            adjust_method = adjust_method,
                                                            adjust_target = adjust_target,
                                                            set_seed = set_seed,
                                                            seed_number = seed_number,
                                                            verbose = specific_verbose)
      savelist[[row]] = specific_scores
      countdown = countdown - 1
    }

  }