dpcReport
In dpcR: Digital PCR Analysis

dpcReport

library(knitr)
opts_chunk$set(echo=FALSE, results='asis', fig.align='center', fig.width=14, warning = FALSE)
# TO DO add warning = FALSE later
library(xtable)

source("server_data.R")

print_dpcrtable <- function(x)
  print(xtable(x), type = "html", sanitize.colnames.function = function(x) x, digits = app_digits,
        include.rownames = FALSE)

new_dat <- input_dat()

Report generated on r Sys.time() using dpcR R package.

Detected input file: r ifelse(is.null(input[["input_file"]][["name"]]), "none", input[["input_file"]][["name"]]).

if(!is.null(input[["input_file"]][["name"]])) {
  cat("md5 checksum of the input file: ", digest(input[["input_file"]], "md5"))

  if(!identical(dpcr2df(raw_input_dat()), dpcr2df(input_dat()))) {
    cat("\n\n**The input was modified manually in dpcReport application.**")
  }

}

File format: r ifelse(is.null(input[["input_file"]][["name"]]), "none", input[["input_type"]]).

if(input[["data_summary_table_rep"]]) {
  cat("## Data summary table    \n\n")

  source("./data_summary/summary_input.R", local = TRUE)
  print_dpcrtable(res)

  cat(readLines("./data_summary/data_summary_table1.md"), sep = "    \n")
}

if(input[["data_summary_scatter_rep"]]) {
  cat("## Data summary scatter charts    \n\n")

  source("./summary_plots/summary_plot.R", local = TRUE)
  p

  cat(readLines("./summary_plots/data_summary_scatterchart2.md"), sep = "    \n")
}

if(input[["data_summary_scatter_rep"]]) {
  source("./summary_plots/summary_exprep_plot.R", local = TRUE)
  p
}

if(input[["data_summary_test_counts"]]) {
  cat("## Compare runs    \n\n")

  cat(readLines("./test_counts/test_counts1.md"), sep = "    \n")

  source("./test_counts/test_counts_res.R", local = TRUE)
  print_dpcrtable(res)

  cat(readLines("./test_counts/test_counts2.md"), sep = "    \n")

  source("./test_counts/test_counts_group.R", local = TRUE)
  colnames(dat) <- c("Run", "Assigned group", "&lambda;", "&lambda; (lower CI)", "&lambda; (upper CI)", 
                     "Experiment name", "Replicate ID", "k", "n")

  print_dpcrtable(dat)
}

if(input[["data_summary_test_counts"]]) {
  source("./test_counts/test_counts_plot.R", local = TRUE)
  p
}

if(input[["data_summary_test_counts"]])
  cat(readLines("./test_counts/test_counts3.md"), sep = "    \n")

if(input[["plot_panel"]]) {
  cat("## All arrays    \n\n")


  arrays <- adpcr2panel(new_dat)

  for (i in names(arrays)) {
    single_array <- arrays[[i]]

    cat("\n\n###", i ,"   \n\n")

    df <- calc_coordinates(arrays[[i]], half = "none")[["ggplot_coords"]]
    df[["selected"]] <- rep(FALSE, nrow(df))

    source("./plot_panel/plot_panel.R", local = TRUE)
    print(p + ggtitle(i))

    source("./plot_panel/test_panel.R", local = TRUE)

    cat(paste0("Array name: ", i, "<br>    ",
               "Complete Spatial Randomness test statistic (", HTML("&Chi;"), "): ", 
               round(res[["statistic"]], app_digits), "<br>    ",
               "Df: ", res[["parameter"]], "<br>    ",
               "Complete Spatial Randomness test p-value: ", round(res[["p.value"]], app_digits), "<br>    ",
               "Method: ", res[["method"]][1], "<br>    ",
               "Alternative: ", res[["alternative"]], "<br>    "), sep = "")
  }
}

if(input[["poisson_distr"]]) {
  cat("## Probability distribution    \n\n")

  for(single_run_id in colnames(new_dat)) {

    cat("\n\n###", single_run_id ,"   \n\n")

    single_run <- extract_run(new_dat, single_run_id)

    source("./prob_distr/single_run_moments.R", local = TRUE)

    print_dpcrtable(mom_tab)

    source("./prob_distr/get_kn.R", local = TRUE)

    source("./prob_distr/plot_density.R", local = TRUE)

    print(p + ggtitle(single_run_id))
  }

}

if(input[["R_code"]]) {
  cat("# R code    \n\n")
  cat("The R code below may be used to recreate reported results.")
  source("r_code_gen.R", local = TRUE)
  cat(paste0(all_lines, collapse = "\n    "))
}