R/print_summary.R

In dpcR: Digital PCR Analysis

# SUMMARY - droplet, array ------------------------------
#summary workhorse + plot, should be not called directly by user
print_summary <- function(k, col_dat, n, print, run_names, exper_names, replicate_names, assay_names,
                          v = v, uv = uv) {
  
  sums <- cbind(do.call(rbind, lapply(1L:length(exper_names), function(single_id) 
    data.frame(experiment = rep(exper_names[single_id], 2), 
               replicate = rep(replicate_names[single_id], 2),
               assay = rep(assay_names[single_id], 2)))), calc_lambda(k, n, v, uv))
  
  nexper <- nlevels(exper_names)
  nrun <- length(exper_names)
  
  #removed re-ordering
  #sums <- sums[order(sums[,1]), ]
  #rownames(sums) <- 1L:(2*col_dat)
  
  if (print) {
    k_print <- ifelse(col_dat < 5, k, 
                      paste0(paste0(k[1:4], collapse = (", ")), ", ..."))
    cat("\nNumber of positive partitions:", k_print, "\n")
    n_print <- ifelse(col_dat < 5, n, 
                      paste0(paste0(n[1:4], collapse = (", ")), ", ..."))
    cat("Total number of partitions:   ", n_print, "\n")
    cat("\n")
    cat("Number of runs:       ", nrun, "\n")
    cat("Number of experiments:", nexper, "\n")
    cat("\n")
    print(head(sums, 20L), row.names = FALSE)
    if (col_dat > 20)
      cat(col_dat*2 - 20, "rows ommited.")
  }
  list(partitions = list(k = k, n = n), summary = sums, nexper = nexper, nrun = nrun)
  
}