peak-type-summary-report.Rmd

---
title: "Peak Type Summary Report"
author: "`r system('whoami', intern = TRUE)`"
date: "`r format(Sys.time(), '%B %d, %Y')`"
output:
  html_document:
    keep_md: true
    df_print: paged
params:
   input_dir: "/path/to/peaks_dir"
   input_items: NA
   plot_height: 8
   plot_width: 8
   dir_mode: FALSE
   id_dirname: FALSE
   out_dir: FALSE
   tss_dist: 3000
   is_report: TRUE

---

```{r setup, include=FALSE}
# ~~~~~ PARAMS ~~~~~ # 
plot_height <- params$plot_height
plot_width <- params$plot_width
input_dir <- params$input_dir
input_items <- params$input_items
dir_mode <- params$dir_mode
id_dirname <- params$id_dirname
out_dir <- params$out_dir
tss_dist <- params$tss_dist

knitr::opts_chunk$set(echo = FALSE, warning = FALSE, fig.width = plot_width, fig.height = plot_height)

# external file with functions
source("peak-summary-tools.R")

# set 'is_report' after loading tools
is_report <- params$is_report

# ~~~~~ FUNCTIONS ~~~~~ # 
```

```{r run, message=FALSE, echo=FALSE, results=FALSE}
# ~~~~~ RUN ~~~~~ #
# get input items; either files were passed or dirs were passed
if (isTRUE(dir_mode)) input_items <- find_all_beds(input_items)

# tsprintf('Input Items are:\n')
# tsprintf('%s\n', input_items)

validated_items <- sapply(input_items, validate_file)

# tsprintf('%s', validated_items)

if(file.exists(".Rdata")){
    # load(".Rdata")
    summary_output_list <- summarize_beds(bed_files = validated_items, tss_dist = tss_dist, id_dirname = id_dirname, out_dir = out_dir)
    save.image()
} else {
    summary_output_list <- summarize_beds(bed_files = validated_items, tss_dist = tss_dist, id_dirname = id_dirname, out_dir = out_dir)
    save.image()
}

```

```{r print_report, results='asis', message=FALSE}
for(i in seq_along(summary_output_list)){
    sampleID <- names(summary_output_list[i])
    summary_output <- summary_output_list[[i]]
    
    # names(summary_output)
    # [1] "pipeline_output" "bed_file"        "process_file"   
    
    # names(summary_output[["pipeline_output"]])
    # [1] "plots"    "peakAnno" "annoStat" "tss_dist"
    
    # names(summary_output[["pipeline_output"]][["plots"]])
    # [1] "covplot"     "plotAnnoPie"
    
    # start Markdown section
    mycat(sprintf('# %s \n\n', sampleID))
    
    # path to bed file
    mycat(sprintf("Bed file: %s\n\n", summary_output[["bed_file"]]))
    
    mycat(sprintf("TSS distance: %s\n\n", summary_output[["pipeline_output"]][["tss_dist"]]))
    
    # print plots
    print(summary_output[["pipeline_output"]][["plots"]][["covplot"]])
    mycat("\n\n")
    
    ## need to run the function for this plot to print again for some reason...
    plotAnnoPie(summary_output[["pipeline_output"]][["peakAnno"]], main = summary_output[["pipeline_output"]][["plots"]][["plotAnnoPie_sample_title"]])
    mycat("\n\n")
    
    
    # the upset plot printint is busted need to figure it out later; 
    #     
    #     Error in gridPLT() : Figure region too small and/or viewport too large
    # Calls: <Anonymous> ... upsetplot -> upsetplot -> upsetplot.csAnno -> par -> gridPLT
    # print(summary_output[["plots"]][["upsetplot"]])
    # summary_output[["plots"]][["upsetplot"]] <- arrangeGrob(upsetplot(summary_output[["pipeline_output"]][["peakAnno"]], vennpie=TRUE))
    # # print(summary_output[["plots"]][["upsetplot"]])
    # grid.draw(x = summary_output[["plots"]][["upsetplot"]])
    # text(x = 0, y = 1, summary_output[["plots"]][["upsetplot_sample_title"]]) # add a title
    # grid.show.layout(gl, vp=viewport(width=1.25, height=1.25))
    # upsetplot(summary_output[["pipeline_output"]][["peakAnno"]], vennpie=TRUE, vp = viewport(width=1.25, height=1.25))
    # class(upsetplot(summary_output[["pipeline_output"]][["peakAnno"]], vennpie=TRUE))
    
}
```

# Session Info

```{r sysinfo}
sysinfo()
```