A quick R Markdown HTML report template that will make a barplot and table with the number of peaks in all peaks.bed files in the target dir.

[[Example Output here]]

./compile-report.R "/path/to/my_peaks_dir"

• -n: Name of report file to output (e.g. -n foo outputs foo.Rmd and foo.html)
• --height: Height of the boxplot
• --width: Width of the boxplot

NOTE: Large figures may not be displayed at full size when viewing the HTML, try right-clicking and selecting View Image.

You can try it out on the included test data:

./compile-report.R test/

Output the report file as test-report.html with a 8x8 boxplot

./compile-report.R -n "test-report" --height 8 --width 8 test

• R version 3.3.0+
  • ggplot2
  • DT
  • scales
  • optparse
  • tools
• pandoc 1.13+