---
title: "dpcReport"
author: "Michal Burdukiewicz, Stefan Roediger"
date: ""
output:
html_document:
css: report.css
toc: true
---

# dpcReport

```{r echo=FALSE, results='asis'}
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 <- change_data(input_dat(), as.factor(rep_names_new()), as.factor(exp_names_new()))
```

Report generated on `r Sys.time()` using [dpcR](http://github.com/michbur/dpcR) R package.  

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

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


```{r}
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")
}
```



```{r}
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")
}
```

```{r, fig.height=(5 + 0.3*nrow(summary_exprep_plot_dat()))}
if(input[["data_summary_scatter_rep"]]) {
  source("./summary_plots/summary_exprep_plot.R", local = TRUE)
  p
}
```

```{r}
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)
}
```

```{r, fig.height=(5 + 0.3*nrow(summary_exprep_plot_dat()))}
if(input[["data_summary_test_counts"]]) {
  source("./test_counts/test_counts_plot.R", local = TRUE)
  p
}
```

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

```{r}
if(input[["plot_panel"]]) {
  cat("## All arrays    \n\n")
  
  
  arrays <- adpcr2panel(new_dat, use_breaks = TRUE)
  arrays_unbroken <- adpcr2panel(new_dat, use_breaks = FALSE)
  
  for (i in names(arrays)) {
    single_array <- arrays_unbroken[[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 = "")
  }
}
```


```{r,eval=TRUE,results='asis'}
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_dpcr(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))
  }
  
}
```


```{r,eval=TRUE,results='asis'}
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    "))
}
```

# R Session

```{r,results='markup'}
sessionInfo()
```