Open rbutleriii opened 1 month ago
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:
spatCellCellcom
## 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 } }
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: